Well as you've already mentioned, AMD's APUs are proving perfect for small media servers and HTPCs. Like Chevron mentioned, many people go with the HP N40l Miniserver (there's an
entire MyBB thread dedicated to it), which uses a low-power AMD Athlon x2 15W dual-core CPU, a mini-ITX board and can fit up to five drives inside this tiny, tiny chassis. The only caveats are that you need discrete graphics and you'd have to output sound using HDMI, unless the PCI-E 4x slot on the board isn't locked for HP's special access card:
HP Proliant N40L Microserver @ R 1999 (you can get it cheaper through Esquire, the MyBB thread details how)
MSI HD5450 1GB DDR3 @ R320 or
INNOVISION GT210 1GB DDR3 @ R333
Western Digital Caviar Red 2TB SATA @ R1248
Total: R3580
You can then add drives on from there - note that you'll be limited to software RAID if you want a RAID 5 array with five drives. Windows makes a total muckup of this because Microsoft chucked out Storage Spaces from Home Server, so their latest implementation is a little tricky and that's where Linux steps up with the better solution -
RAID-Z. Its the best solution if you're aiming for something small and quiet. There are other, more expensive setups but if you're only delivering media and you have everything with a compatible HDMI port, then this is the solution to take. If you're running Linux, take the GT210. If its Windows, go for the Radeon.
The APU setup, on the other hand, offers both multi-media and gaming capability. I'd recommend...
AMD Trinity A10-5800K @ R1547 (or the
A10-5700, its the more efficient choice)
MSI FM2-A75MA-E35 @ R816
Kingston Hyper-X DDR3-1866 4GB @ R274
Seagate Barracuda 500GB SATA @ R603
Cooler Master Elite 360 @ R306
GIGABYTE PoweRock AX 400W @ R361
Total: R3907
One thing, obviously, is that if you're going for the APU, Linux is out of the question if you're going to be making use of its gaming capability. With Steam making its Big Screen work better and better with console controllers, its going to be easier to become a couch potato with the benefits of a full-fledged PC in similar proportions to a console. Get a Xbox 360 or PS3 controller (and bluetooth adapter) and you're all set. You'll still have to buy a Windows license though. I left out a DVD drive because you can decide whether you need one or not - even a Blu-Ray drive would work in here, its your choice as to how far you want to take this. Intel's currently the best bet if you're going with a ITX board and chassis, but it will be quite a bit more epensive.
It could be that the lists haven't been updated. Which board and which CPU are you looking at?