I have all my projects tracked in OmniFocus now. It's basically Getting Things Done codified into a program. It also basically rocks.
I have a plain text file for the longer-term stuff... I think I'm going to end up rolling that into OmniFocus so I do exactly what you said you need to, keep the goals in sight. I end up not really looking at that list as often as I might need to.
I've also started doing what I did back in '02 when I lost the most weight. (Every year since then has been basically a wash.) I'm writing down everything I eat. Not so much to track exact numbers, but that's what I used to do, and nothing else has really worked consistently.
Then I also dump my weight into a spreadsheet... hence how I know I haven't really been moving toward that "weigh less" goal.
Somewhat round about, and probably a bit late... I'd been meaning to write this post for a while now. In any case, there it is.