If you mean rotoscoping in the "original" 80's music video sense (video footage -> drawings), as opposed to the current-day use of the term, rotoscoping (removing subject from background), then I don't know if commotion is the best tool for the job. Someone correct me if I'm wrong, but in all my time using commotion, I found it's strength to be in the area of matte creation, or rotoscoping objects/subjects out of footage. While a powerful paint program as well, I haven't found it to be especially useful at making video look like drawings.
Waking Life used custom software designed in-house to aid the artists in drawing over the footage. However, it was still mostly a frame-by-frame process. Depending on how detailed and stylized you intend to make your footage, there are some filters that most NLEs or Post-FX software packages have-- such as Posterize or Threshhold-- that can give your video a drawn, painted, or cartoonish look. Otherwise, you would have to take it into a program with a good paint engine and go frame by frame and draw over each frame (After Effects and yes, Commotion). If you use AE or premier, then you could even export your footage in the Adobe filmstrip format and open it in Photoshop to draw on each frame.
There's a really good intro to the techniques Sabiston used on "Waking Life" in the DVD's special features section. It's a short doc that shows the software & the techniques used to make the film.