I've been using Tracks (http://getontracks.org/) now for quite a while and am pretty happy with it. The downside is that you have to host it yourself or pay a small fee for a hosted version. But it's pretty powerful, implements the general GTD stuff without being slavish, and has some nice new features like recurring tasks and a iCal link. Not sure what your needs are for nesting exactly - most to-do apps allow categories/lists/projects, but most don't let you do true hierarchies.