[helpermethod]

Like others have already noted don't put too much thought into how to organize things. Keep it as simple as possible. This way you'll spent most of your time doing fun stuff (at least for me that would be writing code).

I'll host all my side projects on github. To keep track of bugs and new features I use github's issue tracker. Besides that I carry around a programmer's journal (some small paper notebook) where I write down new ideas, code snippets or concepts.