I've been over the tech specs for both the high-end mac mini with the fusion drive and the mac mini server (http://store.apple.com/us/browse/home/shop_mac/family/mac_mini) and I cannot find more than a single difference; the server has two HDDs (oh, and it ships with os x server installed).
Am I missing something or are you paying $200 more for a second HDD? Or $150 more for a 1TB fusion drive vs 256GB SSD and 1 TB HDD?
Best Answer
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:
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:
Total: $948.94
Hassle of doing it yourself: Priceless