Stephen Lorenz offers a new set of WWII naval wargames rules called Seas of War. The set is professionally done and presented in pdf format. It also includes the data on a huge number of ships of the period.
The Jim Bowens Disturbia Yahoo Group has free rules for the Gotterdammerung WWII-Horror game.
Matt Fritz has these free wargames rules for gaming the Battle of Midway. The rules are designed for 1/700 ship and airplanes models but Matt also provides paper counters and airplanes.
Crossfire is one of the more innovative — and more enjoyable miniatures games I’ve played. But everyone who plays it seems to have their own house rules. Tim Marshall has a set of house rules that have to be the most comprehensive I’ve seen.