Ohhh, good topic
Lots of games, mind if I list a bunch, since I can't say there's one that's "The best"?
Flashback, so unbelievably good, nothing these days comes close... damn gotta get myself a new Amiga.
Dune 1&2, completely different gameplay, but I loved both of them.
The XCom's are in on the list, obviously, unlike most people(it seem at least) I like both of them.
Fallout 1&2, damn they're good.
Freespace 1&2, see above
Loom, good ole game I played on the Mac a long long time ago, damn good adventure game
Syndicate, Syndicate Wars was good too, but the original is better.
Elite II, wonder why I didn't think of this earlier, definately one of the best games ever, and I played it on the best computer ever, my good ole Amiga, PC's don't hold a candle to Amigas