Capturing flash: Replay Media Catcher. Hands down the best. They have a war going with Adobe. Whenever they think they've blocked flash rippers, Replay quickly turns out an update.

As far as converting, I'm a do it yourself kind of guy. FLV Extract, Avisynth and lots of assumefps and convertfps sort of things.

If you don't want to spend a lot of time on each clip, you can try Riva FLV Encoder http://www.rivavx.com/index.php?encoder&L=3 or the very popular Total Video Converter: http://www.effectmatrix.com/total-video-converter/