After a couple of years with the previous rig, I've built a new quiet yet fully 3D-capable PC. This is used for work, multimedia, and games, all in one box. Not strictly a HTPC. Sorry about the photo quality--it's all my old Nokia can manage.
Stress testing data (at around 19 C room temperature):
Antec Fusion with Tri-Cool fans swapped out for 2 x NoiseBlocker BlackSilent PL2
Core i5 2500
Scythe Big Shuriken with Scythe S-FLEX D
2 x 4 GB RAM
MSI H67MA-E35 (B3)
MSI Radeon HD 6950 2 GB Twin Frozr II
Intel SSD 320 120 GB
Seagate Momentus 5400.7 in SQD
Plextor Blu-ray burner
Asus Xonar Essence ST
Windows 7 Pro x64
Due to the size of the graphics card, the warranty on my enclosure is no more. A part of the hard disk cage was cut out, and the top cover had to be bent out of shape due to the stupid placement of the GPU power connectors. Having owned the NSK 2480, I knew every space where I could apply damping meterial, which i did. I used a bitumen+felt panel in most places, with just bitumen wherever there wasn't enough room. The bitumen+felt panels are anti-vibration, and anti-high frequency at the same time--very handy. Notice how the SQD is not screwed in. The threads didn't match the screws Antec provides, so I squeezed it in with more felt damping material. The middle part looked even worse before applying some cable ties (near the sound card, front wall, and hard disk cage) . It's not a coincidence that the Blu-ray drive cable runs at the top--the bottom opening is completely filled up.
About noise: The X-560 fan wasn't active yet. The case fans are all set to spin at around 750 rpm. The graphics card fans are set to run at 20% when idle, with a slowly rising speed curve for higher temps. I'm happy to report that the card never reaches the higher temps--it becomes audible when stressed, but far from annoying. This is nearly inaudible during the day, and quiet enough at night. I plan on making the rig dead silent when idle, but so far I've had no luck with automatic software control, and there's really no room for a hardware solution.