iTunes! You can easily backup from iTunes by right clicking on the iPhone and choosing backup.
When you want to restore your iPhone iTunes will ask you what date backup you want to restore.. http://support.apple.com/kb/HT1414 If you want to keep a little record then whip up an excel spreasheet with the changes you have made on that date.. But to be honest restores are reasonably quick and if you get the wrong one then you can then try the next one!
If you want to backup up your backups then they are located in (assuming windows):
C:\Documents and Settings\USERNAME\Application Data\Apple Computer\MobileSync\Backup
