The Wrath of Farrakhan
Star Trek VII: The Really Last Voyage (Just found this one today)
I'm a hardcore TOS nut, but that doesn't mean I don't love the parodies- and a lot of the early ILC sketches were freaking great. Seriously, go look for more on YouTube. Good times, those were.
P.S. We must restore balance to the Force by making fun of Star Wars, too: Robot Chicken: The Emperor gets the bad news...