Yeah, when Microprose when down the rights got carved up between Atari and 2K (I think because Sid Meier kept some rights and started a new company called Frixis that then got bought by 2K, could be wrong though)
Then Atari themselves went bust and rights were up for grabs again, someone on these forums found a legal document that listed what Tommo got (Tommo have recently re-branded their games on GOG to 'Retroism' in association with Night Dive), the remaining ones that the list suggests Tommo could still bring are:
Tommo:
Across the Rhine (Microprose - Atari - Tommo)
Air War series (1942: The Pacific, European) (Microprose - Atari - Tommo)
Command H.Q. (Microplay/Microprose - Atari - Tommo)
Elite (Firebird - Microprose - Atari - Tommo)
Falcon (a.k.a F-16 Fighting Falcon) series (Microprose - Atari - Tommo)
Fleet Defender: The F-14 Tomcat Simulation (Microprose - Atari - Tommo)
Gunship series (Microprose - Atari - Tommo)
Knights of the Sky (Microprose - Atari - Tommo)
Lightspeed / Hyperspeed series (Microprose - Atari - Tommo)
MicroProse Entertainment Pack Vol #1: Dr Floyd's Desktop Toys (Microprose - Atari - Tommo)
Orbiter (Spectrum Holobyte - Microprose - Atari - Tommo)
Sentinel, The (a.k.a The Sentry) (Firebird - Microprose - Atari - Tommo)
Starlord (Microprose - Atari - Tommo)
Stunt Driver (Spectrum Holobyte - Microprose - Atari - Tommo)
Task Force 1942 (Microprose - Atari - Tommo)
This Means War! (Microprose - Atari - Tommo)
Virtual Karts (Microprose - Atari - Tommo)
Weird Dreams (Rainbird - Microprose - Atari - Tommo)
But that's just the Microprose ones
Check pages 74 and 75 of this for the full list:
http://docs.bmcgroup.com/Atari/nysb_1-13-bk-10176_313.pdf