Which files to save with timecapsule?

Hello,

I'm using time capsule to save both my desktop and my portable.

In both cases I wonder which files should be saved?

What I mean by that is that I see see no reason to save system files which take up a lot of space and that are updated regularly.

I would make a clean reinstall if I had a system related problem, and would only restore my data afterwards.

Easily it would be saving my user folder and its subfolders, and I have copies of applications in the app store or elsewhere in the cloud. But what about mail and application customizations? Mail especially intrigues me. I use mail with many different mailboxes but as far as I can see the mail data in iCloud only occupies the size of my iCloud account.

I find the apple documentation extremely sparse on both of the subjects (TimeMachine & iCloud).

Thank you in advance to anyone that can and will help.

Lars C.