Mac OS reinstall - what to backup for manual restore?
You will find that TimeMachine is generally inclusive as far as selecting data to back up.  If you take a stock TimeMachine configuration and don't omit anything (supposing your disk is large enough) you will be able to


Perform the backup
Remove the backup disk
Wipe the disk
Reinstall the OS
Reattach the backup disk
Reboot


And all should go smoothly.  In the initial configuration dialog on rebooting, you will find a page that asks you if you want to migrate your data, of which one of the options will be from a TM backup.  This will result in a very cleanly migrated system with very little changed as far as the individual user goes.

But your question was more specific:  Are there data files that you should specifically opt-in for a Mac Backup?  Yes.


Applications folder 

Prior to TimeMachine, I would always kick myself for forgetting the /Applications folder in my backups.  Mac apps generally don't modify items in sub-directories of the Applications folder, so if you're trying to get out of a potential corrupted Application, there's little to be concerned of.  TimeMachine by default includes this.
Application Support/Preferences

Varying heavily from application to application, but generally, most applications look to the ~/Library/Preferences/ and ~/Library/Application Support/ folders for configuration and "temporary" files.  This will accomodate #3 on your list.  TimeMachine by default includes this.


You will likely find that TimeMachine is very capable as a method to make a non-bootable shadow copy for archiving purposes.  If you use it, you should have no issues retrieving any old data ex-post (barring external forces like a bad drive etc.)