I’ve struggled with managing my todo lists and have bounced back and forth among many different applications and even paper notebooks! Recently I decided to give 37signals‘s Backpack as there are a few Mac clients and the web interface is excellent. I’m quite impressed with it and their free account seems to meet my needs at the moment. Browsing it on the iPhone works quite well and now I have my todo lists wherever I go (as long as I have data coverage). Others probably have the same issue organizing todo lists; I hope that this current solution will work for awhile.
Have you tried either one of these? They are both excellent:
http://rememberthemilk.com
http://toodledo.com