Thanks for the help everyone, but I'm still not 100% it's clear. As an example, take this situation and then answer my question.
I have an iPad which is due to be replaced. The iPad contains apps, no music or videos, possibly some calendar data and has had it's settings changed in line with general use.
I launch iTunes by holding alt and clicking the icon in the launcher. This prompts me to choose a library or create a new one. I create a new, empty iTunes library just for this iPad.
I plug the iPad in, do not Sync it but instead just right click on the iPad in the iTunes sidebar and select Backup. Once this is done I unplug the iPad and take it to the Apple store, where they swap it for a new one (the old one had a dodgy Home button BTW).
Step 4 or 5 of setting up a new iPad (after selecting the language etc.) gives you the option to restore from backup. I choose it, plug the iPad into my Mac and select the backup I made earlier.
So, here's my question: Will the iPad now be identical to the one I just returned to Apple?