After trying a lot of different software, I went with
Wondershare DVD Converter Ultimate. It is easy to use, very customizable, can preview what you are about to convert, can set mark ins and outs per clip (in case your dvd has a single file that contains multiple episodes), and best of all you can queue up conversions... not just for one dvd, but for many dvds (if you have your dvds already copied to a drive). The queue feature was important to me as I am usually converting anime dvds with multiple episodes per dvd. I select all the episodes, set what I want each filename to be, queue them up and walk away. Wondershare supports multiprocessors and will process two items in the queue simultaneously.
I use the following settings:
640x480
h264
2000kbps
29.97fps
128kbps AAC audio
The output mp4s look as good as the original dvds. I kept the resolution at 640x480 instead of 720x480 so that I can also load the movies onto my video iPod, although I still haven't tested if my iPod will accept video bitrates > 1500kbps. Each of the anime episodes are about 22 mins long and come out to 280-350mb.
And before some says "you should of used handbrake, it's free" I've been using handbrake for a long time. Although it is great for a free program it does not provide the ease of use or quality that this Wondershare program does. If you don't want to spend any money, use handbrake. If you plan on processing a lot of videos and are willing to pay for a better experience, I recommend Wondershare.