I think it’d be pretty cool to have online video editing tools that could take Youtube URLs (with the #t parameter) and durations for sources, and then a couple of audio channels.
I’m pretty sure you could build it by capturing out of the rtmp stream the way youtubedownloader-ey things do, then you could just run some command-line video encoding software on the pieces, stitch it up as an flv, and give it back.
Sounds hard, but fun. Maybe a Christmas project.