good ideas, I try to do something similar in emacs org-mode, it just tends to get unwieldly after awhile.
Aye, +1 for org mode. I too use org-mode extensively. Perhaps you should try using a combination of custom TODO capture templates, custom agenda views, and/or org-mode's built-in sparse tree generation to help filter through the noise in your (undoubtedly sprawling) orgfiles directory. Not that I've fully implemented this myself, of course, but it's all on the roadmap to org nirvana...