The main difference is documentation. The mplayer documentation has it all there (although I wish it had more actual examples). It was frustrating getting going and I tried the various GUI frontends to little avail. However once I had actually read through the documention I was able to come of with some command lines that work and everything has been good since.
The gotcha on mencoder is the default output format is AVI (which confuses vcdimager) even if your copying a mpeg stream to fix the errors. A simple -oaf fixes this.
For anyone interested I keep track of various command lines on my wiki page for easy reference:
Still it never hurts to have more than one free software tool for these sort of things ;-)
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