A few of my choices:
Asari (Mass Effect series): A race of biotically (psionic) strong individuals who appear attractive to members of pretty much every other intelligent alien species. Asari have only one "gender" and reproduce by "merging" biotically with other sentient beings - regardless of species. Asari exude sensuality, are highly charismatic, and can blow stuff up with their minds. Why do they fit well? Becuase they're basically a good guy sci-fi version of the drow. And people like drow.
Quarrian (Mass Effect): I call them "Space Jews" jokingly - they have been exiled from their homeworld, they have semitic names, they are wandering space in a migrant space fleet, and most other people don't trust them (as they are blamed for unleashing a mechanical scourge upon the galaxy). I like them because they are highly allergic to their surroundings, and so have to wear space suits around other air-breathers. Also, it's pretty cool that they're these great mechanics and they have this great racial goal of reconquering their lost homeworld.
Troll (Shadowrun): Shadowrun Trolls rock because they're big, nearly bulletproof, but not necessarily dumb brutes. They find themselves typecast as enforcers, and have to fight their biological form (large size and a preference for living underground) to exist in urban society. They draw a parallel (at least, for me) for minorities in the post second world war, often finding themselves into criminal activities simply to make a living. They're a big bruiser race that cannot use its natural assets to fight its biggest enemy - racism.
Replicants (Bladerunner): Better than humans in every way, and yet used as slave labour. They have fake memories that they can't necessarily make heads nor tails of. And they have a four year lifespan - and as they get older, they get more neurologically unstable. They practically SCREAM "Playable PC race".
Changeling (Eberron): Shapeshifters work perfectly in a sci-fi setting - especially if there are technological ways to discover their shapeshifting. Couple that with social paranoia, and changelings become this great, noir race. They remind me of criminal undergrounds and resistance movements.