Sorry to bring up an older thread, but for those that used Handbrake to convert videos, what settings were successful for you. I have tried several including some suggested on the handbrake site, but have not been able to copy the video files to the iPad, but can copy to my iPod classic w/ video (3rd generation). I can view the movies in either iTunes, Quicktime or VNC.

I am not converting DRM protected videos.

Per Handbrake suggested settings were:
Use Normal or High Profile
Picture:
Anamorphic: Loose
Display Size 640X480 (trying to keep within more standard just to see if I can get it to work).
Video Filters: Off on all settings
Video H.264 (or MPEG-$ FFmpeg)
FPS: Same as Source (import shows 23.976)
Constant Quality 60.78% RF:20
Audio: Default: Automatic
Subtitles: left as default
Chapters: tried with and w/o chapters identified
Advanced: left as default

Resultant video is:
Codec: avc1
Resolution 720X480
Display resolution 720X480
Frame rate: 14.982520
Audio
Codec mp4a
English
Stereo
Sample Rate: 48000 Hz