I wrote a small script
which offer some option just to have the file setting saved and add 2 lines in that for special functions. Some help online will give usage instructions.
Mainly it work with version 2.5.6. It may run without the X running, to gain some processor time.
About the addition lines is for allowing different file estension and additional command line setting.
Mostly just move into the video folder and launch the script, this will take all avi and convert into mp4 (AVC) FAAC.
Unfortunately I cannot test it fully, I'm running on a netbook now