I am about to rebuild my Windows Home Server. I have 3 hard disks that I am going to put in the server:
Except for the size, the drives are identical. Which drive should I use as the primary boot drive? And why?
Personally I'd have the smallest drive for the primary boot. Simply because this leaves the two larger drives solely for data. If the drives, apart from size, are the same there should be no real difference in speed.
What's the problem with using the smallest?
That way you'll have more space for a large amount of data on the others, while the system itself will have enough space on the smallest disk.
(Needless to say that I'd recommend having separate drives for system and data)
I've chosen the biggest. Why? Because that's the least likely to change. I had WHS on the tiny 500 GB that came with my machine at the time and when it was time to update the drive, moving the Windows Installation took some work that I would have loved to have avoided.
When I reinstalled later, I created a 120 GB Partition on my 2 TB Drive and used that as boot, because I know it'll be some time before I replace that drive.