Much of the earlier stuff is fairly generic. Classic Space doesn't imply, really, that these guys are anything other than astronauts exploring the Moon, and possibly other space bodies. When the subthemes started happening, though, they got more interesting.
Blacktron (both varieties) were definately villains. Other villainous subthemes were Spyrius, UFO, and Insectoids (originally planned to be a villainous organization for the Rock Raiders... but see below), while Mars Mission and Space Police 3 have "bad guys" embedded within the theme (making the reboot of the Space subthemes after the Star Wars hiatus seem more like self-contained units.)
The Space Police (1, 2 and 3), Unitron, and Roboforce subthemes are the "heroic" guys; the good guys of the LEGO space universe. All of them are some kind of space law enforcement, with Unitron having an almost (but not quite) militaristic feel to them.
A lot of subthemes also seem like civilians: the original Classic astronauts, Futuron, M:Tron, Ice Planet, and Exploriens. The astronauts of Life on Mars and Mars Mission don't seem to fit the paradigm quite so cozily; they abandon the "space opera" feel of the other Space subthemes, and instead come across as a more "hard SF" tone, or at least the attempt at such. Also they seem to be a more near-future, almost realistic astronaut and vehicle vibe to them. Well, Life on Mars does anyway. Mars Mission is a more localized space opera with human astronauts fighting off Martians. I'm not quite sure that those two subthemes can be reconciled with the rest of the subthemes.
Some other themes, though---not overtly space, fit in fairly nicely with the Space theme. Two town themes, Launch Command and Space Port, have a astronaut feel, but today's astronauts, today's space shuttles and satellites, etc. An interesting counterpoint, even if all you do with them is mix the parts into your parts bin. There are a number of other themes that are overtly science fictionish in nature, although not set in space, that could also concieveably be reimagined into the LEGO Space universe. The various Aquazone themes: Aquanauts, Aquasharks, Aqua Raiders, Hydronauts and Stingrays are futuristic undersea guys, and even include alien humanoids, or something of that nature. I'd like to think that besides airless Moon-like worlds, the LEGO Space guys may also have found a habitable planet completely covered in water, and that's where these guys live. The Exo-Force theme is based on Japanese manga/anime about big giant robots and the guys who pilot them, so it's also a good fit with Space. I'm not sure where they fit; possibly a militaristic subgroup that is at odds with itself (there are two factions within Exo-Force.) The Rock Raiders and the Power Miners are two themes that have people driving futuristic drilling machines under the earth and finding rock monsters already living there. This could be another civilian group, easily enough, and I think that they'd work well anywhere within the LEGO Space universe as such. Given the fact that the Insectoids were originally going to be a Rock Raiders "bad guy" and later became a Space "bad guy" I think the ties already exist.
What would I do with this pretext; this unification of the LEGO Space subthemes and a few other sci-fi feeling themes, into a coherent setting?
I'm not sure yet. But I might toy around with the idea a bit more before I move on to something else.
Also: just for fun, I included a really slick picture of some guy's LEGO creation of a shipyard, with a ship under construction.