Star Wars Mod (X-Wings! Whee!)
B5 Mod (if this is possible)
Perhaps an adaptation of the Adamant Mod for SEIV
Farscape
Battlestar Galactica
Space Battleship Yamato (hey, it's possible, right?)
Battlefleet Gothic
et cetera.
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O'Neill: I have something I want to confess you. The name's not Kirk. It's Skywalker. Luke Skywalker. -Stargate SG1
Well, anything with spaceships is possible.. within reason Making new races, ships and weapons is relatively simple. There is a "quest" scripting system that can be used to set up special encounters and events, although it'll probably take a while for people to learn.
Mod support will likely be done on a website or a forum (like right here) and it'll grow over time. There are way more things you can do in WW than in SAIS, so trying to cover it all at once in a manual type thing would take a long time to write... Not to mention it's impossible to anticipate everything that modders will try to do.
So when people start fiddling with the game we'll try to answer their questions and keep all the information in one place where other people can find it. We also have various notes written down while developing the game system that may be useful although they'll take a lot of cleaning up and editing.