Well there are a few Indie Developers creating games under this genre.
Gratitious Space Battles (Or something like it): This has cartoon like 2D graphics but is really fun.
Star Trek DAC: Not sure, but this really is an old school game. Enjoyed it.
Sins of a Solar Empire: One of the best strategy games I have ever played. Not sure if this fits in the genre, but you control space ships.
Space Empires V: Average game, but you may like it.
[Edited by HonestGamer, 2/22/2011 9:23:39 AM]
Star Trek Bridge Commander Game..is old..but its a very good game. regarded as one of the best of its series.