What is the difference between a Mac mini and a Mac mini server (late-2012)?
You have to decide what you want in terms of storage, performance and OS since there is no option to have 2x1TB drives in the $799 model and there's no option to have a 1TB Fusion Drive in the $999 model.

Essentially, you're paying $200 more to get OS X Server and for the ability to have a second hard drive (doing it yourself is an option if you can follow guides on iFixit and have the tools and accessories required).



Choose the $799 model with:


A 1TB Fusion Drive - $250
OS X Server - $19.99


Total: $1068.99 (but you'll have a faster drive but half the storage space of the default $999 model).



Choose the $799 model with the default 1TB drive:


add another 1TB 2.5" 5400 rpm drive - about $80+ (approximate cost from newegg)
OS X Server - $19.99
The Mac mini Dual Hard Drive kit from iFixit - $49.95  


Total: $948.94
Hassle of doing it yourself: Priceless