StingingVelvet: DEUS EX JESUS CHRIST.
This.
But also, if I may:
Arcanum: of Steamworks and Magick Obscura. It's steampunk, which is sci-fantasy.
Wasteland: It will make your eyes bleed, however.
Mass Effect: Really, do play this if you like Sci-fi RPGs. It's not going to be looked back on as the greatest sci-fi RPG of all time or anytihng, but listen to the music. Enjoy the character interaction. And try not to sieze up every time you have to drive the Gorram Mako somewhere.
Xenosaga: if you have the ability to tolerate the amazingly overwrought atmosphere and hour-long cutscenes (yeah, really) it's not bad. Playstation 2, not PC, unlike the previous ones.
Agree with Anacronox, geneforge, and Shadowrun. Also suggest maybe some uncommon ones like Might and Magic 4 & 5, Disgaea, or Septerra Core which are sort of liek "Hey, magic, but - SURPRISE! sci-fi!"
And as to why there are fewer, it's probably about corporate policy rather than anything much else. RPGs are supposed to have elves, which have pointy ears. So there's magic. You don't put sci-fi in with magic.
That [url=http://en.wikipedia.org/wiki/E.T._the_Extra-Terrestrial]be silly. It would never be any good, or make money.