Super 8/WMG

The alien comes from the same planet as Clover, and was sent to Earth to look for it.
Throwing out a kinda-obvious one here. The similarity in the two different aliens' physiology suggests they are different evolutionary offshoots; the Super 8 alien is to humans what the Cloverfield monster is to, say silverback apes. Thus, the Super 8 alien is the dominant sentient lifeform of that planet. The aliens' space program had them send Clovers into outer space, like we did with monkeys. One of them crash-landed into the ocean on Earth about a thousand or so years before Super 8 starts. The aliens finally gather up enough resources and send off one of their boys to check up on their spacemonkey's status, but drops the ball and ends up crashing his spacemobile just outside the small town of Roswell, New Mexico. The locals discovered the unconscious alien and drag it and the remains of its ship back to Area 51. Two decades later, the main events of Super 8 happen, and the alien finally gets to go back home and tell his buddies what dicks humans are. And then, three decades after that, a Tagruato satellite lands in the ocean, finally managing to wake up Clover.
 * And many years before that, in the same country, another evolutionary offshoot of the same species would come to Earth in search of gold..

Super 8 has something to do with Aperture Science
The interactive teaser inside Portal 2 would lead anyone to consider this. Super 8 will be part of the Half-Life series, pre-Combine. It will show that Aperture Science runs Area 51. Cave Johnson and Caroline will cameo as they are there for a business trip checking up on their only other branch.
 * I support this theory. Remember What state both Portal and Super 8 take place in. Apeture was probably doing some research and whatever they were looking at got loose.
 * Jossed. It wasn't made in a lab.

The creature is a Tank from Left 4 Dead.

 * What else could slam that door down like that?
 * Actually, The new "Sacrifice" campaign shows that a tank cannot break open a train care. One of the challenges involves letting it out so you can kill it and get through.

Joe and Alice are half-siblings.

 * Alice is probably a bit older than Joe, and her father had unfinished business with Joe's father. Alice's mother isn't mentioned any more than that she "left." It could be that Alice's mother divorced, then remarried and had a child with Joe's father, then died in the accident. Alice's father still showed up to the funeral reception to try to apologize to Joe's father about what happened, even though he was only indirectly related to it. that and Alice's reaction to the video of Joe's mother makes it seem like she has some of her own connections to Joe's mother.
 * And with that, my 'ship has sailed...
 * Jossed, although Alice's father and Joe's mother have a surprising connection.
 * Not Jossed - the canon connection and this WMG are not mutually exclusive.
 * When Alice's father says that her mother left them, I think he meant "stormed out", not "left me and married another guy right here in town but still was nice to me". And Joe and Alice don't look alike. And they would have known. And the dynamic would have been different.
 * Joe's mother may have dated Alice's father for a while in the past or something, and that's why they seem to have known each other so well.

The creature and his ship will cameo in Star Trek 2

 * Super 8 takes place in the same Alternate Reality as J.J. Abrams' Star Trek.

The creature's species is related to the Cloverfield monster.

 * It has a slightly similar body, but, whereas Clovie didn't appear to be. Perhaps Clovie is to it what chimps are to humans.
 * Word of God is that the monster from Cloverfield was a frightened infant that went on a rampage because it was looking for its mother. It's possible that both are sentient, but that Clovie just wasn't mature enough to understand the subtleties of, whereas the Super 8 monster was a fully capable adult. The difference in age could also explain the slight differences in the two creatures' physiologies.
 * Though Cooper is very big, he isn't nearly as large as the Kaiju-sized Clover. It would be odd if the adults of the species were smaller than the infants, unless if they shed their bigger infant bodies like some insects do. Or Cooper is a midget by its species' standards, which would be pretty amusing.
 * The midget thing isn't unheard of. Hell, NASA won't take astronauts who are above a certain height because smaller people maneuver better in cramped spacecrafts. Maybe the space program from Cooper's home planet works the same way.

The creature communicates by electricity

 * Okay, easy stuff first: the alien obviously has one hell of an electrical field, and extremely fine control over it, thus how he flickers lights, et cetera. Here's the tougher part; he uses this knowledge and ability to communicate with humans. Think about it; he's an alien from a completely different evolutionary tree, how does he tell the doctor and Alice that he's scared and homesick? (My) answer: when he grabs the professor, he is able to "feel" all the electrical impulses running through his system, and, based on this circuit diagram, is able to send some impulses of his own. Now, he has no idea of the specifics of what he's doing, he just knows how the reaction to certain impulses looks. I may be wrong, but I believe claustrophobia is one of the more basic neurological responses in humans; all he would need to do is trigger it for a moment in the doctor's and Alice's brains and let them fill in the rest. He may not know how claustrophobia feels, but he knows it has to do with being trapped in a space and not wanting to be there, so he figures it's the closest match.

The White cubes are nanobots

 * That's why they can shapeshift. The cube form is a blank mode, though the exact form is more a design thing for the race.

The alien's view of humans was due to its initial telepathic contact being with a military scientist

 * It basically divided adult humanity into "enemies" and "expendables" (see below as well).

The alien classified kids as innocents, thus they were never in actual danger from it

 * It was never actually revealed that the alien intended to eat Alice -- it had only captured her and was taking her down when the Goonie Squad triggered their distraction.
 * It efficiently picked off the adult members of the party in the tunnels, but left the kids alone until they cornered themselves, and...
 * It was receptive to Joe's message, rather then simply tearing him apart.

The alien is actually an evil Magnificent Bastard

 * The sole reason we "know" the alien is misunderstood is because a few humans managed to get a psychic link with the monster, which supposedly showed its true intentions. However, that means that we're basically supposed to take the monster's word for it. In actuality, the monster came here to scout Earth so his species can come here to Kill All Humans and Take Over the World, but ended up crash landing and captured by the military. As a result, the monster brainwashes Dr. Woodward, pretending to be Not Evil Just Misunderstood, turning the scientist into a brainwashed pawn, whose actions eventually allows the alien to escape. The Colonel is actually the Only Sane Man who realized that the alien is indeed a threat to Earth, and goes after the monster with military firepower to try and contain it. However, the monster ends up overwhelming the military, and escaping (allowing the children to live because the kids will forget about the fact that the alien killed many innocent people and will only tell stories about the alien's "real desire" of "just wanting to go home"), where it will hook up with the rest of its species to prepare a full on invasion of Earth, causing The End of the World As We Know It.

Carey grew up to be Michael Bay.

 * Carey has blonde hair and loves explosions, similar to Bay. He moved to Hollywood and changed his name to Michael Bay.
 * Yes. It also explains to obsession with aliens and metal.

The alien was part spider-based.

 * It had multiple limbs and used some sort of webbing stuff to string people up as snacks for later.
 * When This Troper saw the glimpses of it over the movie, it looked very tarantula-like... Plus it burrows like some tarantulas do.

Carey has no father

 * Joe and Alice's fathers hug them at the end of the film, but Carey's is nowhere to be found.
 * Only explanation is that he doesn't have a father that cares about him.
 * Only Jack and Louis snuck back into town to find their children, the families of the others were still in the shelter on the military base.
 * By that logic, I guess Martin doesn't have a father either? Nor does Preston? Just because we don't see their parents doesn't mean they don't EXIST.

The white cubes are Companion Cubes.
Even not playing the games, this was my immediate thought.

The 1979 amateur film contest was the same one as in Ida Makes a Movie.
Which means they either lost to a 5-year-old, or were in a separate age group.

The alien used the runaway dogs as scouts.
The missing dogs that the civilians were complaining about were found in a circle surrounding the town. My first thought was that they were just running away, but it seemed to me that there may have been a degree of military precision to their movement. If they were just instinctively avoiding the alien, I think their movement would've been more random, clustered together in packs, or they would've ran back home to protect their families. I believe that the alien made physical contact with the dogs, formed that psychic bond, and through the dogs sympathizing with the alien or the alien's threat of force, recruited the dogs to scout the town and surrounding area. Considering that the alien is completely unfamiliar with the territory, scouting around should be the first thing he does.

The alien is a Lurker, before Zerg assimilation
Because, you just have to look at it! Not only the shape, but the burrowing nature. In Starcraft the Zerg are stated as being members of different species that have been assimilated into the Swarm. The Lurkers were once a technologically advanced species, but eventually were assimilated by the Zerg, and their DNA stored, as a latent form, into the Hydralisk's genotype.