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.
Star Trek: The Dice Game is a solo, print and play game in which you manages the crew of the Enterprise through various mission challenges.
The Heavy Metal Wargaming site has some counters for use in starship games set in the Star Trek: The Next Generation universe.
Warhammer Star Trek is a fan-created modification of the Warhammer 40K rules. I ran across these when looking for Star Trek rules to use with my newly painted 15mm figures.
The classic Star Trek shuttlecraft Galileo is available as a free paper model.