Depends on how you want to do it. The way I was taught was to use a program like Quicktime Pro that can break a movie into individual picture files (
I believe it's File>Export>Image Sequence or something like that), open the files in Photoshop or whatever you use for digital imaging/illustrating, and paint whatever you're doing. Then put all of the images back together in Quicktime and call it a day (
if I recall correctly, it's Import>Image Sequence, then you select the first frame of the video. From there you need to tweak the frames per second, video quality, etc.)
You could use other programs, like Flash or perhaps AfterEffects (
both of which would involve importing the video and drawing over it on a new layer.
I never played with AfterEffects enough, but I'm pretty sure it has some vector tools you can work with), but no matter how you do it, you're going to be drawing over each individual frame.
That's just the general explanation, though. So no, there's no program E-Z Rotoscoping Program out there.
It's tedious as hell