Core Game Development Studios offers a set of free wargames rules called Timeline. From the author: Timeline Skirmish is the skirmish game covering all historical ages and into the far future. This game is meant to be fast and furious.
universal
The General Purpose Wargame
David Medlock offers The General Purpose Wargame, a set of semi-skirmish level wargames rules for simulating battles from the Stone Age to the Victorian.
JAGS Revised Free RPG Rules
JAGS stands for Just Another Game System and is described as a “rules heavy” universal RPG system. It’s gotten some notice around the ‘net and is available for free as a pdf or you can pay to get a print version.
Savage Worlds Showdown Alpha Rules
PEG has released the latest version of Savage Worlds Showdown, their universal skirmish rules. It’s available for a free download.