I finally got around to encoding season 3 of Arrested Development using Handbrake. Since I had some trouble encoding 2 of 12 episodes (resolved by getting the latest DVD43 and Handbrake), I ended up encoding a couple episodes using both Handbrake and Videora iPod Converter. It could be the settings I used, but both were 100MB and had the same audio settings, but the Handbrake-encoded version had noticeably better quality.
The difference is really only noticeable when the video is resized. Here are some screenshots from the last episode encoded with Videora and Handbrake, and zoomed in with Photoshop.
The overall picture is much smoother. Also, since Handbrake works directly from the DVD, it keeps the chapter markers in the video. And no temp files! Hooray for Handbrake!
I suppose now I need to re-encode the first 2 seasons.