I've tried many systems over the years for implementing GTD (Palm Pilot, MS Outlook, Evernote, One Note, paper) adding scripts and tools like autohotkey. For me by far the best system is org-mode in emacs, but getting proficient in emacs is not trivial. For me at least emacs also seems to work much better under linux, and org-mode works better if you use emacs as your email client. This is a good reference

http://doc.norang.ca/org-mode.html