Gilmore Girls/WMG

Lorelei and Rory are secretly lovers
Get Squicked out all you want but I know it, You Know it, hell even Family Guy knows it and the 2 titular Gilmore Girls are really just too friendly and comfortable with each other for it to be just platonic "familial closeness". Im sorry if this theory disturbs some fans but somebody had to say it.
 * 'Family Guy did it' should not be justification for anything. Even breathing.
 * It's more of an In-Joke though, as Daniel Pallidino executive produced both on his wife's show and Family Guy. Still, kind of a disconcerting joke.

Dean lied about his background and is actually from Wales
In "Rory's Dance," he refers to Tristan as "Drystan." One might be tempted to think that it was just a put-down, but "Drystan" is actually the Welsh equivalent of "Tristan" (a Pictish name).
 * Probably more "Dristan" than the former; Dristan being an American cold remedy which nobody has heard of since 1989.

The Gilmores and the Forresters have a history that goes back to the Civil War era
That was why Richard immediately disliked Dean: not because he was from a different economic circle, but because he was Irish (Forrester is a Celtic name). Dean's ancestors clashed with Richard's because Dean's were allied with the Fenians (a group composed of Irish expatriates and Confederate soldiers) when they tried to take over Canada following the Civil War.

Honor, Logan's sister, was behind the Huntzbergers' cou against Rory
Honor had a fiancee that the Huntzbergers had an intense hatred for. She strategically got Logan and Rory to go to the dinner to get their attention off of the engagement announcement and focus on chastizing the Gilmore, who they seemed to dislike. If you notice, she seemed rather speechless that Logan even had a girlfriend in the first place, but seemed to perk up at the fact that she was a Gilmore.

The show is told from Rory's perspective, and she is actually a complete jerk
Every time it seems like someone is being mean to Rory for no reason (Example: Paris in Season One), it's only because Rory changes the story to make her the good girl. She intentionally knocked over Paris' diorama on her first day of school, she manipulated Dean into cheating on his wife...You get the idea.

The show is told from Rory's perspective, and is her fantasy because her real life is horribly depressing.
Her mother got pregnant young and ran away from her rich parents to live in a town where no one knew them; Rory is very intelligent but can't get out of her small town where no one understands her. In her fantasy world, her intellect is well-respected by everyone and earns her several scholarships to various prestigious schools she could only dream of outside of, you know, daydreams. She has an incredibly and unrealistically close relationship with her mother and grandparents, whereas in her real life she is terribly bitter with her mother (for running away from her grandparents when her grandparents were rich and could have paid for her tuition) and her grandparents (for not paying for her schooling and getting her a better life). Everyone understands her and is very witty, intelligent and entertaining; everyone loves her. Her entire town has enough money for everything despite most of the characters being in working-class and menial jobs in a very small town with not much of a tourist population or major exports or outside traffic. The entire show is her highly unrealistic daydream wish to help her compensate for how shitty her life is in actuality.

Kirk is a combination of Lucas the Brachen Demon and Mars from Angel.
The Powers-That-Be attempted to save their lives by combining the two of them.

Stars Hollow is one big mental institution, which explains all the eccentric people living there.
Luke is the warden, which explains his Only Sane Man status. Just before the show started, it was discovered that Rory was able to somewhat-function in a regular school environment, so she was allowed to leave the town to go to Chilton. Lorelei also has a deal that allows her to leave once a week for Friday night dinner with her parents.

Richard Gilmore is an older version of 11
The bow tie and the eccentricity gave it away. He's either an older version of 11 or a Meta-Crisis 11 that's been living on earth for a long time.

Mitchum Huntzberger is a Manipulative Bastard
I always thought that Mitchum Huntzberger was awful to Rory (because, seriously, "doesn't have it''" is so vague it really doesn't make sense as an honest criticism) because he wanted her give up her dreams, marry Logan and turn him into someone who could inherit his empire. After all he made such a big show of giving her a job in the first place, why would he shut her down like that unless he was trying to gain something from it.
 * I got the impression that the Huntzbergers weren't all that keen on Logan and Rory marrying in the first place, so why would Mitchum go out of his way to force Rory to give up her dream? If anything he would encourage her, he'd surely know that Logan wouldn't be able to settle with a high flying journalist.
 * Or, maybe he's actually doing Rory a favour. He's seen interns come and go, he's got years of experience, I'd imagine he'd know who had the talent to be a journalist, and who didn't. And let's face it, Rory didn't. She was shy, she only followed direct instructions, and she never took initiative; Mitchum even notes that she would make a wonderful editor.

Lorelai and Rory aren't actually Big Eaters
While it's always implied that they eat a lot, we never actually see this happening. They'll barely touch any food in front of them, and then abandon it completely without a second thought. They might order a lot of food at Luke's or from takeout places, but they'll waste most of it. It certainly explains how a nearing middle-aged woman can appear to eat so much and stay so thin. Rory admittedly gets a pass because she's still a teenager.
 * That actually seems consistent with their personalities - excitable but easily distracted. They also seem to have a lot of leftover take-out boxes at home, so perhaps that is where the extra food goes. However, in that same instance it's shown that they often mix-up the old/new leftovers, and/or just throw it away because they've gone bad. Wouldn't this practice be fiscally irresponsible? (And you'd think Lorelei would have better habits after she'd run away with Rory and had nothing.)
 * This answers the question of how a single mother affords to eat takeout food every night of the week. Even with Christopher helping out, Rory doesn't have a job and Lorelei is only the owner of a small B&B. Yet she has a rather nice house to pay the mortgage on and could only afford to enroll Rory in private school and college with her rich parents' help. Solution: they order a ton of Chinese food and live off it for the rest of the week because they forget to eat.

Stars Hollow is protected by a Hinzelmann-esque creature

 * And that's why it's so idyllic and perfect and beautiful. And Taylor Doose is the town's guardian kobold.

Lorelei is a Troper
Come on, she would practically go hogwild for this site. She'd love to point out every single for every single movie or tv show.