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This will probably get buried but I got a few of em for ya.
Syndicate Wars: Game was mind blowing for the time it was released.
Black and White 1/2: I know, more Peter Molyneaux. Everything else has been mentioned.
Jade Cocoon 1: Not 2. One was extremely unique and you won't find another game like it. It's the coolest monster merging game I've seen and has an endless dungeon.
Dungeon Crawl Stone Soup: It's old but not old. Went open source and has been developed over some time by the community. It's much more newbie friendly these days.
Warlords Battlecry 3: Holy cow the races, persistent hero progression in an RTS. It's age shows though.
That's all I can pull of the top of my head right now that I haven't seen mentioned, though I didn't skim every single comment.
Edit: Just remembered Tyrian existed. Oldschool Schmup that had a good SP campaign and multiplayer.
Mmm syndicate wars.
Is Black and White still in copyright hell?
Seems like it.