As an old timer, I remember more sets of rules gone by the board, but every once in a while a new one that looks promising comes along.
The Forge of War yahoo group (at least for the next few days) has a set of skirmish rules linked to the 40k background. The set is a cross between some of the Rogue Trader and Necromunda. Small groups of troops per player, scenario based games, mini campaigns as a basis of play.
Did I mention free download? The only hitch is the yahoo group will be 'going dark' as the owner will be migrating to a new service soon. So if you want to get a pretty good set of rules for very small level sci fi skirmish, give these a look!