Eureka/WMG

The Artifact was an artifact.
Why? why not.
 * Well, we do know that they share the same universe, though this artifact seems much more powerful than the average Warehouse 13 artifact. This WMG is entirely possible.
 * The man who disappeared in the artifact room, is played by the same actor who plays Artie.
 * I choose to believe it's the other way around with the Artifact being responsible for the Artifacts

Following the Season 1 finale, Eureka is caught in a time pretzel.
After Henry arrives from the future to save Kim from an accident in Section 5, the timeline splits. In one timeline, he saves her, but the Temporal Paradox begins destroying the universe. In the other, he is thwarted by the Jack from the disintegrating future, and the universe-destroying paradox is prevented. He then erases Jack's memory of the other timeline and applies for a job at Global -- perhaps to access the Time Machine again?
 * The revelation that Jack has some fragmented recollection of Henry wiping his future memory will probably feed into this, but it could either straighten it out or twist it even further.

The series takes place in the Stargate Verse.
Jack Carter? Clearly, a brother or distant cousin of Samantha Carter. (His first name is a coincidence.) Given the usually more advanced tech that SGC has access to, this also implies...
 * Along with the appearances from SGC personel (see below), the season 4 premiere had the main cast time travel caused by (technology plus) solar flares
 * How do we fit Senator Wen/Camille Wray into this? Twins? Sisters? Clones?

Eureka is a sanitarium for mad scientists.
The town isn't intended to develop anything because the Air Force already has their Imported Alien Phlebotinum. It just keeps the mad scientists busy so that they don't do anything more dangerous.
 * This explains why we see Daniel Jackson, as well as other SGC personel, monitoring events while thinly disguised.
 * Dr. Fraiser is also from an alternate universe where she married Daniel Jackson.
 * The Artifact is a crippled Ascended Being which the Eurekans accidentally uncovered. The SGC isn't aware of it because of the delusion of top secret-ness at Global Dynamics.

The Artifact's power now inhabits .
We already know, thanks to Stark, that the Artifact's energy can't just vanish; it can only be transferred elsewhere. The
 * She could still have it in some form and it also made her have memories from both timelines (pre-founders day and the current one). It would be a way to return the Artifact storyline and conclude it fully before the show ends with season 5.

The Artifact powers all the improbable technology in Eureka.
A vast amount of the technology in Eureka is soft-scifi at best. There's plenty of stuff like tachyon accelerators, weather control machines, force fields, perfectly humanlike robots, et cetera, that could not exist without breaking or severely bending the laws of physics. The Artifact, as seen in the Season 1 finale, has the ability to do just that. A tiny, tiny sample of the Artifact lets the tachyon accelerator act as a Time Machine -- something that Henry said was impossible under non-Artifact-modified laws of physics. This would imply that some of the crazier machines in Eureka only work in Eureka, when they are in proximity to the Artifact's power. This would mesh with what we've seen. If Eureka is putting out such useful and powerful technology, then someone should have seen it out in the real world. They haven't because it doesn't work in the real world...
 * This means that the residents are "trapped" in Eureka, the only place where the visions in their head can be made into reality, the only place where they can be sane.

Sheriff Carter is one of the few rare individuals immune to Science-Related Memetic Disorder.
Anyone else stuck in Eureka would eventually start making devices that violate the laws of physics and lose all semblance of rational sense. Zoe inherited this as well, although the "rational sense" part is partially obscured by her being a teenager.
 * And yes, the SG-1 staff monitoring Eureka occasionally return to base with the urge to construct zero point energy generators and "really funky giant robots." Fortunately, the Asgard have a cure for that, but it's in rare supply.

Global Dynamics is O2STK from The Middleman.
It makes sense. The technology fits, the situation is plausible, and it gives us the chance for Jo and Wendy to bitch about their respective jobs over drinks. Where is the bad?

Vincent and Fargo are Tropers
They were quite Genre Savvy while watching their Biosphere reality show.

The Artifact isn't from a previous Universe; it's from the end of the current one.
Time Travel is an established fact in Eureka, so why not?
 * This explains how it can contain all the knowledge there is in this universe. If it was from a previous universe, then there would be no reason for it to contain any information about this one. But if it's from the end of this universe, then its history - which to us is still the future - is recorded in it.
 * And with that in mind:

Eureka takes place in one of the future universes from Futurama

 * The forward time machine built by the Professor was thrown forward through the universe multiple times, and The Artifact is from the end of one of the last universes that ended.

Global Dynamics is in direct competition with Veridian Dynamics from Better Off Ted
GD makes everything, VD makes everything. They're the only ones capable of being in business with the other around.

Global Dynamics is in direct competition with Aperture Science and Black Mesa
They all make everything.

Global Dynamics in in direct competition with Massive Dynamics.
They both make everything.

Eureka takes place in the future of Girl Genius.
At some point, the Great War that the Baron is trying to prevent breaks out; then, all the major Sparks will kill each other off. The few surviving weak Sparks, like the gang from the Traveling Show, flee to the New World.

The behavior of most of the scientists on this show is awfully Sparky-- obsessive, not considering consequences, having random bursts of hyper-inventiveness, and creating things that they can't explain, that cheerfully ignore real-life physics, and that make no sense to anyone outside the town. And most of the inventions can't be duplicated.

Nathan will return...
And change his name to Tony.
 * Then he will build a reactor IN A CAVE!!! WITH A BOX OF SCRAPS!!!
 * Word of God sorta confirms this. Nathan was based on Tony Stark.

General Mansfield is a member of the Consortium.
Think about it. Every time something happens, he tries to use it to shut down the town. He fired Carter because Jack kept getting in his way.

Zoe will go into human augmentation/cyborgs
What else combines medicine and robotics?
 * And Zoe will later develop the technology for human personality download, resulting in Jo being turned into the Major from Ghost in The Shell.

Zoe will become an expert in medical nanobots.
The test showed that she has the aptitude to be a roboticist, but she wants to be a doctor so she can help people. So she'll develop robots that do the medicine for her. Human augmentation would make more sense if it were the other way around -- it's what you do if you have the aptitude to do medicine, but you really want to build stuff.

Future Zoe is responsible for her father and her current self being in Eureka
In the pilot episode, Jack and Zoey are in Eureka because another car caused them to swerve off the road... a car that Zoe sees has an alternate Jack Carter and Zoe inside it. The alternate Zoe even waves to Zoe. Obviously, some time in a future time line, Zoe got her hands on a Time Travel device to make sure she spent time in Eureka. And she is careful to drag her father along.

Bringing herself to Eureka may even be the last act Zoe does in Eureka in her personal timeline.
 * Word of God says that Zoe and Jack that caused the crash was them at the time they left at the end of the pilot (after Henry fixed his car and he says goodbye to Jo and the Sheriff). It ended up being cut where it would have shown them going passed their past selves.

Jack Carter is a genius too, just of a different stripe
Most of the geniuses in Eureka are of the Hi INT/Lo WIS variety, nerds who have lots of "great" ideas, but terrible in coming up with practical applications or ones that don't have absolutely lousy side effects. Jack is much more of an engineer type, who prefers to use occam's razor on situations (something that bit him in the ass when he had to be evaluated along Eureka's standards). In a different show, Jack would easily be the smartest of the group, as he can Indy Ploy and/or MacGuyver himself out of any problem. He's just surrounded by a group of people whose intelligence is as much an asset as a liability.
 * So basicly he is a mad engeneer in a town of mad scientist.
 * In a real sense, Sheriff Carter, despite being the contextual village idiot and proverbial civilian (non-scientist surrounded by scientists) is the best scientist in the town because he is the one most closely follows the scientific method as demonstrated by the fact that he is the one who most consistently alters his hypothesis to fit the data.

Eureka is run by Nazis, or at least White Supremacists.
The demographics of Eureka are way off. It might be a stereotype, but there is a reason the stereotype is that there are lots of Jews and Asians in medicine and engineering. In the entire town there doesn't seem to be a single Asian, and most of the people were either at the Church or specifically not at the church in the episode that dealt with religion. Clearly when they say that Eureka was founded after World War II they didn't mean by the Allies.
 * Considering the massive number of former Nazi scientists brought into the United States, post-WW 2, you may be onto something there.
 * Actually, there are a lot of Asians in Eureka. Oh, and the mayor of the town is a black man.
 * As is the head of Global.
 * "Founder's Day" states that Eureka was always "pretty progressive". Which explains why the 1947 natives are less surprised by Jo's being hispanic, than by her Action Girl fighting; and why the soldiers are so willing to flirt with a "Negro" nurse (Allison in disguise).
 * Original troper here. I did write this WMG before "Founder's Day", so it is kind of . This was, as I said, just created as a response to the episode involving religion where everybody in town turned to a Christian church as the only 'religious' answer. And there are not really any Asian /main/ characters, since Kim.
 * To be fair, Christianity -is- a pretty big segment of the American religious population and culture in general. Plus, it's a less 'tricky' religion to write with (a bit of an acceptable target). It'd have to be a very progressive show to have the majority of the cast practicing Judaism or Islam or something else.
 * Most of the American government was white-supremacist to some extent in the days following World War 2. It is possible that the town started off being run by racists but, like most of America, became more tolerant over time.

Fargo is a robot.
And a malfunctioning one, at that. His cryogenically frozen grandfather was an earlier model.

Henry is a Time Lord in hiding. Specifically the War chief
In a town of Geniuses Henry tends to stand out. He has at least working knowledge of basically anything under the Sun. He is brilliant and inventive and managed to figure out how to use the Artifact for a form of Time travel. During the last Time War, the Time Lords brought the War Chief back from beyond as another weapon to use against the Daleks. Being a sound strategist he opted for retreat as a better part of valor.

Knowning that there was Nowhere in time he could realistically hide. He decided to go sideways in space instead of forward in time like the Master. Like the Master he decided to used the Chameleon Arch to hide for a decade or two from the Timelords. But instead in a Parallel universe in his new form of Henry Deacon.

Like Professor Yana, Deacon is what the War Chief is not. Henry is friendly, an idealist and not a big fan of the War Machine. Fortunately for Eureka after his so called friend mind wiped Henry back in the day he forgot about a certain Family Heirloom, a pocket watch he just had'nt gotten around to opening...yet.

Zane and Claudia actually are siblings
After having a falling out with their family due to his criminal record, Zane erased Claudia and their parents' memories of him using a device similar to the one Henry used on Carter at the beginning of season 2. He looked slightly shocked upon first seeing her in Eureka. This was because he never expected to see anyone from his family again after erasing their memories. When he told her there was no such thing as coincidences, it seemed like he knew something she didn't that he wasn't letting on. Plus, it would be a great excuse to have Claudia come back to Eureka or have Zane visit the Warehouse sometime, and it could lead to some great awkward moments between Zane and Fargo.
 * Hmm. Joshua pretty much raised Claudia after they were orphaned...

The new Timeline is an excuse to bring back Stark.

 * Come on, you know it is.
 * This leads to...

Nathan Stark will come back in the eighth episode of the fourth season

 * It is named the "Ex-files", and we don't know what happened to Nathan in this timeline. Allison never actually got to marry Nathan again, so he would still be her ex-husband.
 * Confirmed. And for bonus points, Beverly is thrown in for good measure.
 * And Jossed all along, thanks to

Thanks to Carter, this new Version of Kevin is armed with the power of Common sense.
In episode two of Season four we see that Kevin is comfortable hanging out at Carter's house and stealing his bacon. So, goes to show not only is one of the brightest minds in Eureka thanks to Carter he doesn't overthink and sees the simpler solution. He is more down to earth and practical way of saving the town in The Story of 02.

The time travel/alt universe arc will end with it being reset to the original, founders day timeline by Henry and Carter.
They will be the only people to remember what happened. Allison will not remember getting together with Carter. Henry will again have lost a girlfriend/wife (and for good measure, will probably see her killed off in the first episode after the reset).

Season 4 is really the Season 1 finale, "Once in a Lifetime"
Well, let's think about this. Once in a Lifetime took place in 2010, four years in the then-future, and it's 2010 in this timeline. Going from the start of the episode:
 * Jack and Allison were together. They just got together at the end of The Ex-Files.
 * Zoe graduated Valedictorian. Granted, in Season 4, Zoe's off in college, but she was accepted into college early, rather than graduating from High School first. They may bring her back as #1.
 * Kevin appears to not be autistic; in fact, he's rather sociable. As shown in Season 4, this Kevin isn't autistic at all.
 * For the first half of the episode, Nathan Stark is nowhere to be found. In Season 4, Nathan hasn't shown up yet, and we don't know if he died in this timeline.
 * Henry is married. Sure, it was to Kim in season 1 and to Grace in season 4, but the similarities are remarkable.
 * Jo is with Taggart, not Zane. In The Ex-Files, Jo admits that she doesn't think she and Zane are supposed to be together. And Taggart is supposed to come back this season.
 * "Time Travel", or rather, "parallel universe consciousness travel" was a major component; fixing the timeline. That's basically what's driven Grant this season -- to return home.

The travelers did not alter the timeline, they are in a different timeline
Carter, Henry, Allison, Fargo, and "Doctor Oldspice" are all in a timeline separate but similar to their own. Meanwhile, everyone in the "original" timeline are wondering where the four have disappeared to and/or are working feverishly to bring them back. Other possibility: There has been a massive shuffle of all of these versions of themselves across all timelines, threatening to destroy all possible universes in some phlebotinum loaded manner.

Hallucination Stark is the real Stark.
Two things point to this, or at least to him be different than the other hallucinations. First, he points Jack to where the resonance device is hiding. And, secondly and more importantly, he reacts to the other hallucinations. All the others, especially Tess, do not react to things the other hallucinations say. Stark does.


 * Much as I hate throwing a sapnner in the works, how is it he could react to the hallucinations, even if he was the real Stark? Though, he also knew other things Carter wouldn't, like Starks shoe size and the aforementioned device..
 * He Ascended to a higher plane of existence and lost his fourth wall

Alternate universe Carter was neither in love with Allison nor particularly close to Zoe.
Zoe is really surprised to see him show up at Harvard -- a lot more surprised than he seems to be expecting her to be; he seems to view a random college visit as much more likely than she does. It makes it look like their relationship in this universe never got much past the slightly prickly phase they were in during season 1, maybe because Carter bonded with Kevin instead.

Then, in "Momstrocity", Kevin realizes for the first time that Carter is in love with Allison. If alt-Carter behaved anything like the original, there's no way Kevin could have spent three years around the two of them without figuring it out. So presumably he didn't -- because there was nothing to figure out. Maybe, in the alternate universe, Carter has UST with Jo and is Like Brother and Sister with Allison instead of the other way around? That might also explain why Jo switched jobs...

The plot arc for season 4.5 is going to be a Mars mission.
All the main characters are going to be on it, except Fargo, who gets stuck as Mission Control.

Consider the following pieces of evidence:
 * IMDB has a list of episode titles for 4.5; they include "Liftoff", "This One Time In Space Camp", "One Small Step", and "One Giant Leap" (the last two being the final two episodes of the season, and hence presumably a two-part finale).
 * We've been getting indications for a while that GD is planning to go to Mars -- the terraforming chemical in "The Story of O2" and the biosphere in "What About Bob?" are both intended for a Mars colony, for example.
 * Wil Wheaton has said on his blog that: "Most of my scenes this season were with Neil Grayston and Felicia Day because [SPOILER]."

The titles suggest some kind of space theme to the season, with a moon-landing-type finale. But the moon is accessible enough to Eureka that sending rockets there is literally a school project; another actual moon landing would be anticlimactic. A Mars mission is the next step up, and is a potentially-reasonable length for a seasonal arc, especially if the finale is the landing -- getting from Earth to Mars in a standard transfer orbit takes about 8 months.

If Fargo is mostly interacting with Wheaton's character and Felicia Day's character, and it's for a spoiler-ish reason, presumably it's because either the three of them are the Mars mission, or everyone else is. The "everyone else" theory makes more sense for the following reasons:
 * Fargo is the head of GD. Heads of massive governmental facilities don't get to play astronaut -- they have too much else to do.
 * Fargo is the Butt Monkey. Not getting to go to Mars when everyone else does reinforces that.
 * It's a lot more exciting for the protagonists to mostly be traveling to Mars than for them to be watching other people do it.
 * The idea that Jack Carter would be the first man on Mars has a certain... resonance.
 * The first episode of the new season has them testing a Faster-Than-Light Travel wormhole drive. This kinda makes Mars seem a bit of an easy trip.
 * Fargo was hauled into Washington to try and justify the ongoing expense and mission of GD, so he might be forced to try for the spectacular to keep his position and funding.
 * In the second season, Felicia Day's character reveals that Global Dynamics is going to get a 20 billion dollar grant to build an FTL spaceship to go to Titan. My guess is that the OP is right, if you replace "Mars" with "Titan".

Warehouse 13 (and by extension, Eureka and Alphas) take place in the "Normal Again" world from Buffy the Vampire Slayer.
Magic clearly hasn't overrun the world in Normal Again as it had in the Wishverse and the "What if Buffy died" verse, so the bureaucratic confusion amongst various government agencies ensures that the Secret Service and DCIS are unaware of the Watchers and the Slayer, and the British are still ticked about Warehouse 12 being moved so the Slayer and most Watchers don't know of the existence of the Warehouse. Most of the creators of artifacts put their own brand of energy into the artifacts by the focus and near-ritualistic repetition of what they did (see: witchcraft and its demon-worshipper equivalents), strengthened (or even changed outright) by their public image. Alphas are probably unrelated to magic, and more closely tie into the Mad Science of Eureka and Warren Mears.

As for the thing in Sector 5? It is (among other things) the heaven-dimension equivalent of a Hellmouth. Beauty, comfort, energy, and a Mad Science field come from it the same way dark feelings, demons, and an increased magical field come from the Hellmouths.

All ex-Stargate actors showing up in Eureka aren't different characters, but an AU version of their stargate character.

 * Pretty much all of them show up in a similar capacity to their old SG characters, so they probably just took a different path and their names are different because of the changes in the timeline. Camile Wray was an IOA rep which is basically a politician, and now she's a Senator, a politician anyway.

Warren Hughes from the episode "Clash of the Titans" is secretly working for the Consortium.
At the end of the episode, Relationship auditor Warren Hughes(Wallace Shawn) gave Jack and Allison an ultimatum;. Given that the DOD didn't give Allison this kind of scrutiny when she was engaged to Stark, it's making me wonder if the Consortium is trying to undermine Allison's position at GD after Beverly's failed attempt to hack into her mind to steal GD's secrets. The Consortium is trying to destroy Eureka's Titan program, and taking Allison out of a position of leadership would definitely help in that scheme.

Eventually, on our more of "our" universe characters is gonna get caught and be in trouble for violating the temporal prime directive
Too many of them have told other and/or gotten their brain scanned and/or behaved suspiciously, especially with the senator around.

Carter is an Alpha.
His ability is both in having enhanced "common sense" (more than the rest of the town put together), and in seeing solutions to problems. His drawback is needing things explained that a moderately well-read person would know.

Carter and Allison will marry in season five, after the Astraeus mission returns.
In the animated Christmas episode, "Do You See What I See", they were wearing wedding rings. Christmas episodes take place outside of canon, but this one was still filmed during season five. Evidence:

Holly is still alive.
Because the creators and writers keep saying to trust them. Maybe Beverly somehow saved Holly, and she survived.
 * She could still be in the virtual reality database somehow and she just needs to be imprinted back into her own body.
 * We'll probably at least see her in alt-world, just played by an NPC.
 * During the episode, we got the warning that dying in the virtual world could potentially kill you in the real world because the mind makes it real. But this also opens up the possibility that Holly could survive, if not because of any outside force, than simply because Holly's skepticism in the reality allowed her to ignore what it was telling her.