This one is great. There's "simple mode" which is great and you really can't stuf up, and if you've feeling keen, fairly detailed advanced settings.
http://www.videora.com/en-us/Converter/iPod/
Not free, but uber-cool - use your recent generation Nvidia graphics card to convert videos. This is so fast it's unbelievable. Note: I've used it once (you get 30 free goes at it) and I didn't tweak the settings at all, and it did a very reasonable job. Would probably do a lot better if I played with the configuration. You won't have to leave it running for hours to get a result.
http://www.badaboomit.com/
Turbo