OK, this is what I remember. You played a squad of space marines, and you had to navigate through old space craft in a turn based system. You were up against these horrible alien knock off guys.

And the game was bloody IMPOSSIBLE! Now what on EARTH was it called?

Space Hulk knockoff?

Incubation?

http://www.mobygames.com/game/incubation-time-is-running-out/cover-art/gameCoverId,59358/


Available here on GoG in the Battle Isle Platinum series

http://www.gog.com/en/gamecard/battle_isle_platinum

Space Crusade, perhaps?

Impossible Mission Staring Cruise Tom
Just kidding. ;)
How about Command Adventures Starship? If it had spaceship exploration/fighting too could fit your bill, I know it had on ground combat on alien ships, but, don't remember too much else, its been about 10 years. I do remember that I had fun playing it though for a time.

Yeah, it sounds like either Space Crusade, or the earlier game Laser Squad.

That was it.....Space Hulk. Goooood, that game was unwinnable. I seriously don't think I solved a single level. Man, I deserve another shot at the title. Bring it back Gog.com!