The Warseer forums have an interesting thread on using Games Workshop's Lord of the Rings battle game to run Warhammer 40K skirmish games.
As a kid, one of my favorite book series was Edgar Rice Burroughs' "John Carter of Mars." I can't tell you how many times I've read the first, "A Princess of Mars."
So I was excited to find Green Blood and Red Blood for Mars, a set of rules for mass combat on Mars in the Victorian Age. Now I've got one more excuse to get some of those neat martian figures that are circulating from various companies these days.
The Napnuts offer Captain Arjuns' Starship Combat Rules. These are perfect for recreating your favorite starship battles from Revenge of the Sith, A New Hope, or any of the other Star Wars movies.
Just in time for Revenge of the Sith, the Singapore Napnuts offers Senator Arjuns' Star Wars Skirmish Rules.
Andy Watkins offers Hammers Slammers, a set of generic science fiction rules. Watkins has designed a lot of rules, and in each he seems to have created interesting and enjoyable rules sets.