Trek Movie has a good rundown of scenes that have been deleted from the final cut of J.J. Abrams' Star Trek. One scene, which actually made it onto a trailer but not the big screen version of the movie, shows Amanda (Winona Ryder) and Sarek (Ben Cross) holding baby Spock. Another involves Kirk's alcoholic, abusive uncle. The most interesting and longest cut, though, was a whole subplot showing how Nero managed to escape the Klingon prison planet Rura Penthe. Bits of this one made it onto one of the trailers as well. To see these scenes in full, we'll have to wait for the DVD.
Meanwhile, another collection of clips that did make the final cut has been released, including some extended versions of scenes available earlier and some new footage of the Romulans.