For d20(-derivative): Mutants & Masterminds (Green Ronin). You can use it, sans most powers, for human PCs. You can use it for aliens. You can use it for ships. Since all of these are built using the same system, they're all compatible. You can (fairly) easily adapt it to miniatures play or run battlemat free as in the default (particularly nice for those three - or more! - dimensional space battles).
Alternative: True20 (Green Ronin). Similar to Mutants & Masterminds, lighter but not as flexible. For sci-fi in particular, I'd take M&M, but True20 is also an excellent system. Chargen would be much faster than in Mutants & Masterminds, and it's a more familiar (to D&D players) character advancement system.
Alternative: d20 Modern/Future with d20 Future Tech, Future Player's Companion (Game Mechanics), Blood and Space (RPG Objects) and d20 Mecha (Guardians of Order). d20 Mecha remains the best d20 vehicle construction system on the market, IMO, whether it's for giant robots, spaceships or age of sail clipper ships. This suite is slightly more limited, but still a very solid post-D&D d20 system. Chargen would be easier than M&M, tougher than True20. This might be the best option if you want built-in support for miniatures play. I also reccomend Blood and Fists (RPG Objects) if you want *any* kind of martial arts in the campaign; it's an invaluable resource for all d20 Modern compatible games.
Out of Left Field: Star Wars Minis. A true rules-light alternative. Either slap on the skill system of your choice or leave skills to the players' character backgrounds ala O/A/BD&D, and enjoy truly fast and furious d20-based combat.
Non-d20: Silhouette Core (Dream Pod Nine). A great system for sci-fi with an available setting (Jovian Chronicles) that should suit your target tech level. Considerably more lethal than any of the d20 options, for better or worse. My personal favorite system, though Mutants & Masterminds is, objectively, probably a better design.
