Like most processes, it's better to keep something like this lightweight. "Nested todos" are about as fancy as things get.
I also check the todo lists into the project. Sure, it makes things a little dirty. On the other hand, it saved another person's bacon last year when I was forced to flip ownership of a project over to that person without much warning. (He discovered the todo list, and emailed me a huge thanks).
Todo lists in a wiki can work well to keep a loose team on the same track, too. Again I think the secret is to keep this lightweight.
If you're installing "Whizzy Enterprise TODO" servers or having meetings about how to manage todo items or trying to extract metrics from todo lists, my guess is that you've put too much drama into the process and should take a walk to cool off. :-)