In the never ending goal to make sure I can restore and keep up with my systems' apps and configurations, I started a github repo this year to list them. The hardest thing about this is to make sure I update the repo as soon as I make a change. As long as I do this, I am set.
The goal of the repo is to make it simple to replicate my settings on other machines and to recreate them completely if I choose to "clean install" a computer. The nice thing about iOS5 and iCloud is that I can rely on iCloud backups exclusively. I Will see how well that works when I have to do a restore in the future.
Anyway, feel free to ask questions about my choices and make suggestion. Let me know how you keep up with your settings and apps.