I would suggest you to backup everything (except /tmp). If it is a typical linux machine, the only thing in /home are the user directories and usually neither apache or the server documenter root are in that directory.
If you just want the users home directories go ahead with /home.
else at least backup apache directories so that you can restore them after a fresh linux install.
It all depends on how quickly you want the server to be back up after it goes down and how much effort you want to put into it.
if time does not matter, backup only the specific directories so that you can restore them manually later, but it will take a bit of effort.
Personally I would go for a full backup. provided enough space and since subsequent backups will mostly be differential backups, it is not that much of an issue.