I'm going to work on the assumption that you're going to build a desktop and run it as a fileserver, not a rackmount type server with redundant PSUs, server grade hardware, etc.
The biggest difference between getting an out of the box option and a DIY option is going to be the number of drives you plan on using. Since you're planning on RAID 5, it's going to be tough to find an off the shelf desktop that supports more than 3 or 4 drives in the case. If you want something with much more storage, then you'll want to build it yourself (including a case to accommodate how many ever drives you want).
Of course, if you're thinking of buying an off the shelf server and not repurposing a desktop, then this really doesn't apply.