I didn't answer this cleanly in the post, but I don't there is such a thing. The perfect todo list is the one you can get yourself in the habit of using every day. And that varies from person to person.

For me, that was a text file, and I link to my specific suggestions at the bottom. For others (such as Matt Might) it might be an app like OmniFocus. Or perhaps you like working out of your email inbox.

Follow the fundamental principle: what can you get yourself to actually use and stick with?