That BitFenix Prodigy case looks amazing. I want it.
Looking at the SFF builds linked in the OP, the price is ~1600 for Enthusiast build. Is that because the parts are extremely high end, or because the small form factor necessitates using more expensive parts that aren't necessarily the best?
Also the ram listed is an 8GB Samsung 30nm which has since been discontinued.
Prodigy.
$79
PROS: Lots of room for Air and Hard drives and a 51/2 if you need it. Has plenty of niches that you can shove an SSD into. Cheapest of the bunch. The feet are cool.
CONS: Watercooling is a BITCH that can require heavy modification and particular parts. Won't fit a powersupply bigger than 160mm without looking stupid.
CaseLabs S3
$199 + Accessories
PROS: Will fit pretty much anything you throw at it, the flexbays are awesome, comes in Black, White, Blue, Grey or PRIMER (to paint any colour you want). Amazing build quality from a very well regarded company. This case is something you would get to be able to do anything you want, most flexible of the bunch.
CONS: "cheap" initially but when you enter the world of customizing it the price can really ramp up quick. Kinda large and 'boxy'.
CompactSplash
$150 + shipping
PROS: Specifically designed to be the smallest possible case that will accept a full custom watercooling loop. Each one custom built and custom named, can be ordered in any colour for an additional charge. Only available for a limited time!
CONS: Air cooling options limited. Will not take regular ATX powersupplies at all. Only fits two 2.5" hard drives (4 if you are watercooling your video card and literally tape two together), Only available for a limited time!
Fractal Node
PROS: Beautiful, super duper tiny. Supports 3.5" hard drives and regular sized powersupplies.
CONS: Powersupply outputs fit snugly against longer video cards. Aligning the CPU cooler can be tricky. Very tight space to work in. No 5.25bay.
Here's a couple other cases that aren't listed in the SFF Guide.
The motherboards tend to be more expensive for the ITX, and other parts are more particular (to fit). The Enthusiast build is geared towards the higher end of things. You could bring the price down quite a bit by going 3570K instead of 3770K. And 256gb SSDs are about $50 cheaper nowadays anyway. (And not getting the optional $120 sound card)
The Samsung RAM is amazing if you can find it, but any ram will do if you don't have plans to push its capabilities.