Thanks for the help guys. I'm not doing a big enough job that I considered developing outside of the framework of the game - but if my ideas get any more grandiose I suppose I'll have to consider it.
Todo blocks and change histories are the two main things I was looking for. I'm used to having both a commenting feature and a source protection utility - but as this is strictly a hobby project, I don't have any of the stuff I used to use at work. 
Ah well. I'll just have to start either noting down what I've changed or else keeping a folder full of different revisions. 