I keep everything in Notational Velocity stored in plain text files, which I keep in sync between multiple computers with Dropbox. It also syncs with SimpleNote so I can view/update it from my iPhone or iPad or from the web. Simple, and I can access it from anywhere.

Within the text file, I usually group ideas by type and mark it with a '*' if I implement it, and a 'X' if I decide it's not a good idea/it's already been done/I've lost interest in it. Has worked well for me.