According to TrekWeb, the Star Trek Season 3 Blu-Ray set will include the longer cut of "Where No Man Has Gone Before," which has never aired or appeared on DVD or VHS. (The Youtube video above includes all the sections that are different.) The original cut started with a view of our galaxy, while Captain Kirk talks poetically (in an "Enterprise Log," about Earth and its sun being specks of dust as the Enterprise ventures out of the galaxy. There's also a long scene of the crew stalking down a hallway as the ship goes on full alert, and a bit more Kirk/Spock banter. Not only that, but the opening and closing credits are totally different, with the televised "whoooo-ooooo" music being replaced by some music that sounds more like the show's other incidental tunes.
Given that the season three box set also includes season three, it's good that there's some incentive for fans to buy this thing.
Separately, Roberto Orci and Alex Kurtzman told the Screenwriters Expo in L.A. that they think the next Star Trek movie is coming out in 2012, not 2011 as we've been told previously. Orci and Kurtzman had planned to have the screenplay done by Christmas, but with the new timeframe, they're going to take longer with it. As for what happens in Trek 2, says Kurtzman:
They're established now in the second movie and they're finally a crew so it will resemble what you see in terms of they are already who they are.