Silent Hunter Commanders edition, the one that started it all. Sure the graphics are dated, but it's got everything you need for a good submarine game, and with dos box there's not a computer it wont run on really.
Part of it is nostalgia, as it's the first subsim I played seriously (Gato was the first sub game I played though back on the good old Apple IIE). I put a lot of time in Aces of the Deep as well, but in general I preferred the visual style of Silent Hunter. Are there less "twidily" bits in SH:CE then in SH4 (my other favorite in the series) absolutely, but really if as the the captain I've got one hand on the periscope and the other dialing things in on the TDC I'm not doing the whole "command" thing well. You can do a much more nuanced target approach in SH4 with the map tools available (particularly with mods), but with outside programs you can run a pretty good attack party in SH:CE (you can use the same utilities for SH4 to if you feel like it of course).
-Jenrick