I am a rather large fan of the games.
The Amanda series is RTS, so you'll either love or hate the gameplay in that. I definitely loved it.
I then bought one of the Commander series, where you specifically get to control a ship (like most of the games), and then Starfleet Commander 3. It was a rare copy that I managed to sell for £50 on Amazon.co.uk. It took long enough to find too...
The Legacy I have on the Xbox 360. It's actually not too bad, and the user interface works well enough, until things become hectic. I finished the game twice - I may have to try it on the hardest setting next. I can see the last mission becoming an issue as that was hard in the first place...
Legacy just has updated ships, better graphics and more happening at once compared to the others. I hear it's a little demanding for older PCs though, so I still recommend that you buy the older series/Amada because of that.