I've been using org-mode since 2008. The most stable usage pattern is clocking the work time under the relevant org section whenever I'm working on a project. This gives a nice progress metric and a rough log of what I did and how long it took. Some kind of cross-referenced reading notes system would also be good, but I haven't gotten around to properly setting one up yet.
Org-mode really works on the single-system aspect, though nowadays an organization system really should do mobile integration too. Org-mode has some kind of external app for ios/Android, but I don't know how well it works with the rest of the system.
Related to: Rationality Power Tools
I'm looking to use (or make) something that helps me achieve god-like productivity. In particular, I'm interested in any information about systems that are:
I would prefer not to have a bunch of separate systems if possible. From what I've seen so far, org-mode seems the most promising.