Here’s a link to a set of Dr. Who miniatures rules.
Astral Dreams is a free miniatures game based on the d20 Open Gaming License system. The game’s background is based on a short story of the same name, which involves a war between humans and robots.
The folk at One Page Rules have released a new edition of GrimDark Future, a set of one-page rules (with lots of pages of armies you can also download)
Under the Broken Moon is an RPG based on the Thundarr the Barbarian cartoon series. The game uses a mechanic where you roll a number of dice equal to your trait score and sum the results.
Next to The Sword and The Flame, Warhammer has to be the most modified set of miniature wargaming rules out there. As further proof, I offer: Warhammer Star Trek, a Yahoo groups project designed to use the Warhammer rules in the Star Trek Universe.