I use a plain text editor of my own design. The back end is written in C#, compiles with Mono, and I have front ends written in GtkSharp and WinForms. It treats files in a directory as pages in a notebook, and it automatically tracks history of edits and autosaves every few seconds.

Its primary distinguishing characteristic is that it auto-saves to two files: a plain .txt file, and a .log file containing deltas. Replaying the log file reproduces the contents of the txt file. I can scroll backwards and forwards through the log in the editor, as well as through pages (files) in the directory in modification order. By default, it opens up the most recently modified page.

Whenever I start on a new task or bug, I create a new page (with a single keystroke) and simply start writing out a TODO list or steps of investigation. As I complete items, I delete the detailed text associated with the item (leaving only the header line, moved to a DONE section), or as I discount threads of inquiry, I delete them. If needs be, I can scroll through the deltas, retracing my logic. Works great for refreshing my memory or reloading context when I need to switch to something higher priority.

By convention, I use the first line in each file as a title. I have a single keystroke that brings up a search box; the search box incrementally searches through every title of every file. Files are lazily loaded when opened. I don't browse the filesystem to open files, I open things up by title. If I need deeper search, I can grep the txt and log files in the file system; I haven't had a big enough need to add that feature directly.

The directory is stored in Dropbox for synchronization, which also makes my notes accessible on my phone. It's backed up separately.

Any conflict between .txt file and .log file is resolved by replaying the log, then appending the delta between .txt and result to the log. Thus if I make concurrent updates, or modify text files on my phone, they're still available without losing history.

I use this editor at several levels. I have some high-level pages that track broader priorities in a category, some that act as idea dumping grounds, and lots and lots of pages that involve work specific to a task.

I'm not far from considering linking it to Google Calendar - creating a text convention that can be cheaply scanned for and calendar entries created, for deadlines or whatever.