To start with, he made a deal with the devil (literally) where he got his marriage retroactively annulled in exchange for his Aunt's life being spared. Then Doc Ock possessed him for a while, during which time he got his degree and founded Parker Industries. These days, Peter Parker is beating Tony Stark at his own game, while Ultimate Spider-Man (who isn't Peter Parker) is doing the “friendly neighborhood spider-man” thing.
Oh, and MJ Watson has taken a job as Tony Stark's personal assistant and has recently suited up as the Iron Spider (not sure about the name; but it's the suit Peter wore leading up to the Civil War story arc).
I've seen rumors that the alternate “Renew Your Vows” Peter Parker from the recent Secret Wars event will be showing up again.