First off.. have ya tried DVD43? (
www.dvd43.com ) it will decrypt the DVD on the fly, so you don't have to rip it to the HD and THEN Handbrake it. Eliminates a step and speeds it all up a bit.
As for Handbrake settings, here's mine...
Use the Iphone preset:
Then change...
H.264 (ipod) to MPEG 4
No Crop to Auto Crop
Uncheck Chapter Markers box
leave average bitrate at 960
Leave everything else as is...
Once I started using these settings, I haven't had to RE-convert anything to get it on the Iphone!
Have fun!