TiddlyWiki and unit tests.
For plain bugs such as "seg fault when doing x" I just write a test exposing the bug. This way, I won't forget about a bug even if I don't touch the program in six months. It will appear again as soon as I run the full test suite.
For more complex bugs such as design flaws, bugs from user interaction etc I keep them in my to do list in a TiddlyWiki.
TiddlyWiki is the perfect documentation/note taking tool for projects with a single developer since the entire wiki is in a single self contained html file. Therefore, it requires no installation of any software (except a browser) and you can just keep it with your sources and commit it to your repository for safe keeping.
I keep all notes related to the project, ideas, design notes, to do lists, bugs etc in it. I prefer it to plain text because it's so much easier to keep it neat and somewhat structured without being a pain to use. The ToDo list is the most important item since I never know if I will continue programming tomorrow or in six months and need to be reminded of what should be done. Bugs end up in the ToDo list since they are things that should be done just like "Redesign the crappy back end". When one item (feature/bug/whatever) gets too long, I move it to a separate tiddler (like RedesignCrappyBackEnd) and just link to it which keeps the main ToDo list clean.
When I'm finished with a bug or feature, I move it from the todo list to a "Done" list. In this way, I can keep a simple log of bugs, features and what's been done recently. This can be very handy if you suddenly remember you had a similar problem before but can't remember what it was or how you solved it.
The main drawback is that you can't/shouldn't use it for projects with 2+ developers since it handles simultaneous edits just as bad or worse than a plain text file.
I think it provides the most bang for the buck being almost as simple as a text file but much more structured. I have tried some more sofisticated tools but always come back to TiddlyWiki because of its plain simplicity.
(Actually, I use the MPTW clone which has better tagging)