I use VLC media player to convert video files (flc, wmv) to mp4 for using on ipad.
Here is what I specified:
Video codec: H-264
Audio codec: MPEG 4 Audio (AAC) Bitrate 64 kb/s and another convert with 128 kb/s
The converted mp4 files sync to ipad via itunes. The video is fine though not smooth, but NO audio.