I need a program (preferrably a gui since those seem to be best at compression) which will encode pretty much anything into iPod-compatible h264/x264 which will allow me to customize the screen resolution and bitrates (video/audio). It's OK if I have to go into ini- or whatever files to do it as long as I can actually do it.

meGUI is out since it has some major issues updating and is hence useless. The 3GP hack (the non-hacked version keeps stopping every once in a while to attempt to do some weird thing called "QT3GPPFlatten". When I removed that command line, it just stopped altogether) has issues with framerates lower than 29.97 (25 fps seems OK, but I don't have any long movies which run at that framerate to test, 23.97 FPS movies are obviously out of sync).

Any suggestions?