I used to play the simulator box set as a pert of an RPG campaign. It was good because it was simple and fast. If you needed to resolve some ship-to-ship combat within the course of role playing, you could do it. all you had to do was whip out the maps and counters and you were good to go.
after playing it a while, my players and I did get a little fed up with the pro Federation slant to the ships, but hey, we just changed the stats too make the Romulans, Klingons, and especially the Gorn better.
The computer version from SlightlySilly is lots of fun for me. Its easy to design your own ships. I even make my own game counters and they look pretty good. It has some problems though. The computer opponent has no clue about handling cloaked ships and, (my biggest complaint) is that you can't save a game and quit ion the middle of a game.
as for the STTCS vs SFB debate, well their both OK with me, but for something you can do quickly on the fly in support of an RPG, the simulator is the best!