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.
lego
Mobile Frame Zero Lego Rules
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 Lego Wargames Rules
Brickhammer is a set of free wargames rules for playing wargames using Lego and minifigs.
Minifigz Lego Combat Rules
Minifigz is a set of rules for combat with Lego figurines.
Play Ogre With Lego
Steve Jackson’s Ogre is a classic game. I first got a copy when it was in a small bag with thin cardboard cutout counters. It’s gone through several incarnations since then, but the idea of hordes of GEVs and infantry against a single cybernetic tank. Now Dan Efran has a page describing how to build Ogre pieces with Lego. Its really cool, and I can’t wait until my kids outgrow the things and I inherit them.