Handbrake is what I have used. There is a side panel with a few presets, but I found the default works best. The default settings ran faster and produced a smaller file than the iPod preset. The results does well on my iPod Touch.
After it has read in the DVD's directory there is a pull down menu of the videos on there. The first is usually the movie the extra features, such a "making of" and trailers. There are tabs to set various options, such as including chapters in the export and selection of audio track and sub-titles.
As for region codes, Handbrake will probably work anyway. The main issue is that the optical drive will only allow a limited (5 I think) region changes. (The only way to reset this count is to replace the optical drive.) If you have a DVD player that will play the DVD, a video converter, such as the Elgato EyeTV Hybrid, might be an option