Well it appears I missed out Onyx from the special on open source 3d space games... or did I? With no pointer to a source repository nor a zip/tar/rar of source, or a freeware download of any mention, I can't classify this game as anything other than todoware at the moment. Contact the Onyx developer(s) if you want to beta test the game.
Something I did find a lot of fun was mono, by Binary Zoo. Sadly it's only available for Windows, although I'd be interested to hear if it worked through WINE. It's fantastic fun and really shows it's possible to innovate even though the graphics and gameplay are so simple.
A great freeware title that runs in Linux, with similar innovative qualities, is Bubble Thing. Inflate the bubbles until they burst and see if you can create bubble-popping chain reactions. You can make the bubbles absolutely massive with controlled inflation.
I know this is supposed to be an open source games blog but those two freeware titles really caught my eye (and attention).
Currently the games list is missing a large number of iD-based open source 'stuff' such as Darkplaces, FreeDoom, the Vavoom Engine, OpenArena, Hexen II: HoT, and others. There's a lot of them. I'm working on adding them to the list in a way that does not swamp the rest of the list in the new 3 column layout. Expect it in a couple of weeks.