So this is really great...there's this free website called GoAnimate.com that allows you to make your own Star Trek animations!! The website has a Flash-based animation platform with premade backgrounds, characters, props, music, special effects and more. It's really easy to use, and really fun.
Sorry, only TOS characters currently
If you have a minute, please check out the first episode of a parody series called "The Bacheluhura":