I'm much like you. I used text files and utilities, developing some of my own, but in the end I've fallen back to a simple pen & paper technique.
1) I find it easier to browse written pages. It also seems to tweak some sort of memorization when I need to recall things from long long ago. I doodle a lot, especially during meetings so I can recall when I needed to remember a note that it was written somewhere around the page with a dinosaur wearing a baseball cap in the margin
2) Taking my eyes away from the screen to jot my tasks, is almost like a mental reset. It causes me to slow down and think more about what I've done or will be doing tomorrow
3) It almost becomes an "additional monitor" to have up. No tabbing to a file, no spacing things on desktops to keep the work list above other forms; its just there, off to my left to view.
4) (EDIT) Can't believe I almost forgot what I consider the strongest point... is connecting thoughts. Trying to draw a line between comments I made earlier and something I've done just now is nearly impossible to do cleanly in text IMO. Notes like "See July 4th, 10:35PM" is worthless and requires a new level of focus that a squiggly arrow just accomplishes so much easier. Colouring in a black box above an important note I want to immediately catch my attention when i'm flipping backwards is so much more important to me than any text file organization.