You can edit each preset or add additional ffmpeg parameters in WinFF. If you want total control, then I recommend using ffmpeg or mencoder without a GUI:
Code:
find ~/path/ -iname "*avi" -exec ffmpeg -i {} -pass 1 -b 512k -acodec copy -vcodec mpeg4 -vtag xvid -s 320x240 -flags +trell -f avi /dev/null && ffmpeg -i {} -pass 2 -b 512k -acodec copy -vcodec mpeg4 -vtag xvid -s 320x240 -flags +trell -f avi ~/newpath/{}.avi \;
I didn't test the above code. You will need to change ~/path/ to whatever directory you want to encode from, and ~/newpath/ to the destination directory. I don't use xvid, so you may have to change -vcodec to xvid and possibly omit -vtag xvid.
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