Admittedly, Roswell barely qualifies as 1990s, because it began in 1999, but it was one of the better sci-fi shows I've seen. Among other things, it turned the genre on its head by being told from the perspective of aliens, in the present day, on Earth. It had a lot of things going against it, of course, with network politics being the big one, and season two strayed awfully far into X-Files territory, but it had good writing, good acting, and much like Stargate, it didn't take itself too seriously, somehow managing just the right blend of humor, romance, dramatic tension, etc. And in spite of the main characters being teenagers, it managed to almost entirely avoid the usual teen drama that you'd expect to clog up such a series.
My favorite funny moment had to be when Jonathan Frakes (playing himself) told one of the alien teenagers that he just didn't make a believable alien. And my favorite episode was the Christmas special; it was almost pure character development, did nothing to drive the plot, but it was a breathtaking tear-jerker that gave a lot of insight into the main characters' personalities.
If you haven't seen Roswell, it's worth a look.