My settings:

Resolution: 400x240
Auto Crop : depends on how the original video is formatted. I try all three until I find one that makes the picture look normal.
Frame Rate : 25 fps (box left unchecked, no idea what that's for)
Aspect Ratio : 15/9 (read somewhere here that this is the aspect ratio of the N800 anyway)
Bitrate : 512

Audio bitrate: 96
No resample

I only wish it was able to do a bulk conversion using drag and drop. Instead, I have to manually drop each video into the converter, and after setting the preferences correctly, click Add and repeat.

A bit of a pain when you have around 50 episode of Initial D anime to encode :P