I use text files. (.txt, because I hate waiting for a rich text editor to open, and I hate autocomplete for normal writing) It's the only way to be able to keep track of them. I sometimes write paper notes when I don't have a computer nearby, but I usually don't keep those notes. Sometimes if I think of something I absolutely have to remember as I'm dozing off to sleep, I'll enter it in my cell phone because I use that as an alarm clock and it's always close to my bed. But my cell phone's keyboard makes writing notes really slow, so I avoid it under normal circumstances.

I have several kinds of notes that I make. One is when I'm doing a hard intellectual task and I want to free up short-term memory, I will write things down as I think of them. I usually title this kind of file with the name of the task. For tasks too minor to remember just by a title like that, I just write something like " <project name> notes 2014-06-22".

I also write "where I left off <date>" notes, whenever I leave a programming project or something for a day (or sometimes even before I leave for lunch), because usually I will be forming ideas about how to fix problems as I'm fixing other problems, so I can save my future self some work by not forgetting them.