I will add my standard rant about Star Trek games. 25th Anniversary and JR are the best Star Trek games because they do what Star Trek does best -- tell a compelling story. The same is true of A Final Unity, but the gameplay there was not as well thought out. In other Star Trek games, story may be present, but it takes a backseat to action. Star Trek was never just about action (at least until JJ Abrams got ahold of it). I think it's hard to make a great Star Trek game based primarily on action, just like it would be hard to make a great Star Wars game where action wasn't a substantial component.
On that note, I don't think anyone has mentioned the interactive fiction trilogy produced by Simon & Schuster in the 80's. The Promethean Prophecy and the Kobayashi Alternative were frustratingly difficult to play, but First Contact was actually a very good game, if you overlook some of its faults. It's the only Star Trek game in existence where you can explore the entire Enterprise (but without images, so you have to use your imagination). It also has some great character moments and a pretty decent plot. The plot has some striking similarities to JR, and I wouldn't be surprised if Interplay was influenced by it. These games are not that hard to find for free online, and can be played with DOSBox.
Of course, no post of mine would be complete without lamenting Secret of Vulcan Fury. So this my lament.