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I am about to rebuild my Windows Home Server. I have 3 hard disks that I am going to put in the server:
A. 1TB
B. 1.5TB
C. 2TB

Except for the size, the drives are identical. Which drive should I use as the primary boot drive? And why?

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Neither... get an SSD and run your OS from there. – KronoS Mar 28 '11 at 19:23
I have SSD's on other computers but don't consider it necessary for backup server that does not need to be performant. – Guy Mar 28 '11 at 19:26
Actually the point is, that you're using up space on one of those higher capacity drives that you probably want to have allocated for your data. It'd be better to have a smaller drive for your OS installation IMO – KronoS Mar 28 '11 at 19:34
up vote 3 down vote accepted

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.

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Why does it matter? He can carve out a separate partition for the OS, and that will be the same size regardless of which disk he uses. – Joel Coehoorn Mar 28 '11 at 20:52
If the disks are the same spec they will have the same cache (say 32 meg) - that cache on a 1TB drive will be more efficient than on a 2TB drive. – Majenko Mar 28 '11 at 21:23

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)

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+1 for separate system and data – Dave M Mar 28 '11 at 19:27
Why does it matter? He can carve out a separate partition for the OS, and that will be the same size regardless of which disk he uses. – Joel Coehoorn Mar 28 '11 at 20:52
@Joel Yep, he can do that but placing the OS on a separate disk makes it easier to restore the system in case of a disk failure without needing to touch the data (and vice-versa) – slhck Mar 28 '11 at 20:59

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.

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Agreed. The drive size does not matter, because you'll create a separate partition for the OS anyway. Also, you probably want the operating system on the fastest of your drives, since other factors like network i/o are likely to limit your data speeds. The bigger drive is likely to be a little faster as well. – Joel Coehoorn Mar 28 '11 at 20:52
The drive size does matter, because you'll be stuck with the primary drive longer than the others. – Jay Bazuzi Mar 29 '11 at 6:07

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