Bridge Commander is very good, at least if you put some time into modding it, since the default ship lineup isn't very long. The Starfleet Command games are also pretty good, more similarities to STO than Bridge Commander.
There's also Legacy. Sort of a trimmed down version of Bridge Commander, more combat less managing sensor settings and power distribution but overall similar control and combat. Probably one of the best default ship lineups, but with mods filling in blanks they're all pretty much equal.
Combat-wise, both Bridge Commander and the Starfleet Command games share some definite similarities.
If you're looking for something on a larger scale, there's always Star Trek Armada and its plethora of mods.
The original Sword of the Stars is also good if you're looking for what amounts to Total War In Space with simplified empire management and real-time space battles with customized ships. The second one's still being worked on and has some fundamental game design problems.
If you'd like something large-scale and less dependant on combat, there's the excellent Galactic Civilizations II. Think Civ 4 in space with ships you design and build from various bits and bobs.