Really depends on what you like...
Details on your favorite genre would help.
Hard science fiction is what I like...
And Star Trek, and Stargate... don't watch much else.
I'm not sure if you like hard sf or space operas more.
If it's the first, as in: "weird but mostly scientifically viable, cerebral stuff", then I'd recommend
Texhnolyze and would second
Ergo Proxy. These are both very complex and detailed sf, with some metaphysics thrown in for a good measure. The second one is probably trying a bit too much, but it's still a very interesting show.
There's also the
Ghost in the shell franchise, which is a pure sf, cyberpunk cop flick. There's a couple movies and a
series, made by different people with somewhat different approach.
If on the other hand you preffer space operas, as in:"adventure and drama happening in a generally sf environment", then I'd say
Cowboy Bebop and
Planetes. Keep in mind that both of these keep their action bound in the solar system, so they're not exactly Star Trek-like. Planetes is especially science-abiding, apparently they hired some people from Japanese Space Agency(or something) and it shows.
Note: all links to Anime News Network. You can find detailed reviews there, just keep in mind that these are written by anime fans for anime fans.