BrikWars! is a site dedicated to fighting miniatures battles with Legos. No, I’m not kidding. You have got to see it to believe it. There’s a Lego Napoleonics battle that makes me want to raid my kids’ collection.
Bricks Only Wargame is a set of free wargames rules for wargames using Lego bricks.
Consortium Games offers Minifigz, a two page rules set for battles with Lego minifigs, and similar mini people. I’m going to have to give this a try.
Update: The original link is dead. You can still find Minifigz on the Wayback Machine.
Mobile Frame Zero is a set of free wargames rules (although you can pay, too, if you like it and can get a printed version) for playing games using Lego and other construction toys. It is very well done.
Brickhammer is a set of free wargames rules for playing wargames using Lego and minifigs.