I also use HandBrake for the basic DVD rip. Then for the actual videos, I use
MPEG StreamClip set to these encode 'Export to MPEG-4' settings:
My recipes assuming a 16:9 aspect ratio:
For the Web and so-called SD:
Codec: H264
Single Pass for low motion interviews etc. Multipass for my wobblycam location sequences; B-Frames
Data Rate: 1.1Mbps
640 x 360 px
Deinterlace where needed; 29.97 fps
Sound: MPEG-4 AAC Stereo when music is used, otherwise Mono; 44.1 kHz 128 kbs
For Apple TV and other so-called HD devices:
Codec: H264
Single Pass for low motion interviews etc. Multipass for my wobblycam location sequences; B-Frames
Data Rate: 2.1 to 2.5 Mbps (occasionally I will up this as far as 3.5Mbs if I see pixellation or banding - iterative process)
1280 x 720 px
Deinterlace where needed; 29.97 fps
Sound: MPEG-4 AAC Stereo when music is used, otherwise Mono; 44.1 kHz 128 kbs
Have fun!
Chris