I am planning on setting up a DFS root to house all of our departmental shares, and I also plan on having Home directories that automatically mount through AD profile. We will be using a NetApp for storage. Should I have the home dirs be part of the DFS or does it make more sense to have them on a separate partition/volume of the NetApp?
I wouldn't do it. My two main reasons to do DFSN (DFS Namespace) don't apply to home folders: using DFSR to replicate folders and have AD figure out your closest copy, and second if you want users to have a consistant path to files reguardless of what file server they are on. I love DFS and use it with many clients/jobs but I see little advantage (and maybe some disadvantage) of using it for home dirs. Here's some thoughts in no particular order: