OK you've got a good idea for a game. How do you keep track as you flesh it out?

I write notes in a wiki-style program that I wrote that saves my notes to plain text files. Whenever I code I type down my thoughts as I go so I have a clue what the hell I was thinking when I implemented X. It allows me to just use the date as a comment in my code which I can then reference the large set of notes. I also use it to record any general ideas. If I feel as though it's something that's appropriate for a larger category I create a new page or branch pretty easily. Having the ability to search across files has been quite helpful.

Before I wrote this program to help me manage my notes, I just used a text file.

Exactly what kseh said. You can also do the same thing (note taking) on a piece of paper or even use the comment function in whatever IDE you're using.

I use Trello for tracking things, five lists ("Idea dumping ground", "Ok I'm going to do this", "Hmm not now, maybe later", "Doing", "Done.") I like being able to stick something down via my mobile if I have a moment of enlightment while out and about, and the general simplicity of it versus colossal beasts like JIRA.

High level architectural stuff I scribble out on paper until it's sufficiently crystallised, then it'll go in Visio or similar for reference.

More specific code-related thoughts are either put in comments or if it's actionable, todo tags.

I write a spec. https://github.com/GlPortal/specification