I like to watch flv videos during downtimes using my ipad. Whats a good tool for converting video files and then tossing them onto the ipad. Primarily I've grabbed a few flv tutorials off you tube. I know ffmpeg can do the transform, but it's got one of those "needs a phd in video" to sort out...
I find that MediaCoder works quite well for video transcoding. It has presets for iPod/iPad and runs just fine under Wine.
Once you have the codecs installed, you just need to learn one
ffmpeg command to re-encode your videos:
ffmpeg -i in.flv -vcodec libx264 -acodec libfaac -sameq out.mp4
For help with codecs, I recommend this useful page at Ubuntu help.