Though it's not without its flaws, Getting Things Done by David Allen is at the least a good starting point to personal time management. I also recommend Thomas Limoncelli, Time Management for System Administrators, which addresses specific requirements of many tech workers (programmers too).
From Allen, particularly, the notions of different levels of task (he uses flight/elevation metaphore for Immediate to life-long goals), and of regular review. Information capture without review has very little value.
My first problem with the genre generally is that it seems to presume everything can get done. Actually, no, it cannot, the attempt will burn you out or kill you (see the FT burnout article I'd submitted earlier: http://archive.is/OQSTS). But your planning/tracking system may well (and really should) help you discover your pace, rhythms, limits, and warning signs.
Allen shares my general disdain for computerised trackers. I've settled on bullet journal and index cards, mostly, though I'm still developing my system and tuning it.
Another issue is that many "tasks" really aren't; they're goals, aspirations, large projects which have not yet been analysed, assed, broken down to subtasks, and/or abandoned. Even apparrently trivial items can take far longer than anticipated.
Your personal community -- at work, home, social, commercial, political -- has a tremendous influence. If you are constantly facing opposition or at best apathy to even basic goals or needs, any progress will be exceedingly painful. Changing environments is almost always easier than changing peoole, though if you find the situation unchanged even in new environments, consider looking at yourself and how you respond. My first approach is generally to try to work with or accommodate others, but I'm getting far quicker to push back and demand what I need to function and succeed. That's often the only thing that works.
1. Though in fact took me nearly ten years to get Getting Things Done done, no joke.
Your second point is well taken... maybe the real problem with the genre is that it's much easier to deliver a system that handles discrete tasks, whereas dealing with larger goals or aspirations is too open-ended to design a product around.
I thought GTD had a good idea regarding stuff you can't get done by shoving it in a circular file, and maybe that's what I need to do. Not abandon it, but it's better to not worry about it for a while and come around to it in time.
I'm looking at tools such as vimwiki / orgmode, possibly task-warrior or renind (both CLI task managers) for longer term/repetitive stuff.
On my (linux) desktop I've got a set of general information displayed via xrootconsole, and having reminders there might be useful w/o being excessively distracting.
A script sets up multiple "panels" of information for me -- (randomly selected) RSS feed, weather, essays-in-ptocess (a large part of my To Do), and systems monitoring. That's usually obscured by open windows (and I don't use a desktop file-browser, so this isn't cluttered by file or app launcher icons), but I can check quickly by hiding open windows/reveal desktop.
With CLI reminder/calendar tools, ant term window can show wahat's pending / manage tasks.
This list should be reviewed regularly (but rarely), say monthly or yearly. This way you can let go of the anxiety of forgetting something that is important to you, while at the same time not getting defocused from things that you can do now.