I've used the following method several times to do this.
1) Use ffmpegx (
http://www.versiontracker.com/dyn/moreinfo/macosx/15473) to convert .flv's to .avi's (it should also be able to convert from .swf).
2) Then use quicktime with flip4mac installed (
http://www.flip4mac.com/), to convert it from .avi to ipod format.
The only problem is the sound is just barely out-of-sync with the video (~0.5 s).
cheers