If you have enough space and time, backup these directories in their entirety:
• /Library
• /Users
Plus, any applications (or installers) that are not bundled from Apple, or easily downloaded again.
If you wish to save some time and HD space with your backup, avoid backing up any directory that includes the word "cache" in its name (there are a few of these in every home directory, and they can be quite large). You may also want to consider leaving out the music and picture folders if they are large and you don't need their content preserved.
EDIT:
When restoring data after the OS install, don't copy these entire directories back. You may not actually need much (anything) in the /Library directory. And you'd be better off copying the contents of each user directory back to their new home folder, rather than replace the entire /Users directory with the old one (could save a lot of fiddling about with permissions/ownership).