I use AVPlayerHD as you can play most file types (AVI, XVID, mp4 etc..) not just the iTunes movies. To load files into it, when the ipad is hooked up open the ipad apps pane in iTunes, scroll down to file sharing and highlight AVPlayerHD then drag'n'drop your movies into the file box on the left. Sync then you're done. AVPlayerHD isn't free but is very flexible with regards to movie file types and I've had no stability issues.
Other players may load files in a similar way.
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