Modern Family/WMG

Jay is Manny's biological father.
Manny looks exactly how you'd expect the son of Jay and Gloria to look, even if he's supposed to be adopted. So he isn't. Gloria met Jay 11 years ago when he looked much more attractive. They had a relationship, Manny was born, and when Gloria broke up with Javier she went back to Jay.
 * The only flaw in your reasoning is that 11 years ago, Jay would have looked like Al Bundy.
 * I don't think Jay would look as bad as Al Bundy. Al Bundy at Jay's age probably looks a lot worse than Jay does.

Jay is a mob boss.
We don't know what he does, only that he's rich, so...
 * Cleared up a little in a season two episode where we get to see some of what he does. It's still mostly ambiguous though.
 * Jossed in the Season 3 episode "Hit and Run", where we see that Jay manufactures closets. In the same episode, Manny is doing a school report on The Mafia, and neither he nor Jay act like Jay has any special knowledge of the subject.

Phil is not Haley's father
Would explain why Haley seems to be the odd one out, physically.
 * She has a lot of his other traits though.

Luke will grow up to be a Rorschach like vigilante.
He already doesn't trust the police, and we've seen his semi-violent nature via the squirt pistol. It's only a matter of time.
 * Only to be foiled time and time again by the Boxmaster.

Manny is gay
It wouldn't be too far off for this to be revealed if the show runs long enough:
 * Although this show isn't crazy about gay stereotypes, some do appear: Mitchell is a fan of musical theatre, Cameron is flamboyant and a fan of various pop icons like Cher and Madonna.
 * Manny's "stereotype" is his interest in fashion, or at least in looking sophisticated in suits and other clothes. Remember the puffy shirt?
 * When Jay tries to tell Manny off for something, he most frequently compares him to Mitchell (Manny's poncho and Mitchell's "jaunty scarf")
 * It's probably more likely that Jay's looking for someone to relate to and share his interests with. Note how he gets along in a much more casual way with Cam, in no small part due to Cam being a football fan. Compare this to Phil who's a man-child, and Claire and Mitchell who has very different interests.
 * Although Manny is teased for different reasons (being Colombian, too mature, overweight) when he needs advice about being "different" he most often gets it from Mitchell or Cameron.
 * I always thought Manny's sophistication and interest in fashion were a way to portray him as a very young, modern dandy.

Haley got abducted by aliens and is replaced by an alien replicate
Would explain the massive Flanderization she experienced somewhere around the middle of Season 2.