I've just got my rig back up and running after completing a refit. Changed motherboard, a couple hard drives, case, CPU cooler and modded the case with sound dampening material by Acousti. Using an Aerocool Touch 1000 Fan controller. And got rid of the RAID 0 configuration in favor of a 4 tier hard drive setup.
Full Specs:
Intel Core2 Quad Extreme QX9650 12Mb L2 Cache (3Mb each core)
Asus Rampage Formula Motherboard w/ 1333Mhz FSB with Gigabit LAN (onboard sound card used exclusively for front panel audio connectors when needed)
6Gb Corsair Dominator PC8500+ @ 1066Mhz
ATI Radeon HD5970 2Gb GDDR5 Graphics Card
Asus Xonar D2 Sound Card
Compro T500 T-DVB Digital Tv card
x2 Sony DRU-870s DVD-RW Burners
Pioneer BDC-202BK 5x BD-ROM + 12x DVD±RW SATA Dual Layer ReWriter
x3 Western Digital 500Gb Hard Drives (One used as primary OS and application drive / One used exclusively for downloads/ One partitioned in 2 for use for Windows XP and Vista OS Installs)
x2 Western Digital 1Tb Caviar Black FAEX Drives (One used exclusively for game installs / Other used exclusively for Backups)
Zalman CNPS9700-NT CPU Cooler
AcoustiPack Ultimate Acoustic Dampening Material
Tagan TG1100-U88 1100w BZ-Series Modular PSU (x6 12v rails)
Asus U3S6 Sata III and USB 3.0 Controller Card
x6 120mm Cooler Master SickleFlow Fans, x1 200mm Side Fan
Microsoft Windows 7 Ultimate 64bit Edition
Dlink DGL-4300 Gigabit Router
Iiyama ProLite E2607WS 26inch Monitor (1920x1200 / HDMI)
Altec Lansing FX-6021 2.1 Speakers
Here are the pics with Illustrations (Don't laugh at some of the descriptions... It's my way of keeping organised when all I see in thread writing is HTML code)(Warning, my camera is crap):

Case Exterior

Case Front

Case Side Panel

Fan Controller (BTW... The current temp showing in this pic is not my CPU temp... It's my GFX card temp.)

Case Jacks and Lights

Exterior Top Mount Fans

Monitor/Desktop (Yes, I know it's messy... And yes the wallpaper is a Dreamscape with full rotating Earth) (Update: I have replaced my keyboard and upgraded to the Logitech G510. I have also replaced the mouse and upgraded to the Roccat Kone+)

Front of case with Plates removed.. Foam blocks for sound dampening and help maintain directed airflow.

Internal Components (As good as the cable management in this case is, I just have too much hardware... There was only so much I could do.) Also, while the push lock mechanisms on this case are excellent and far more competent than most tool-less case mechanisms I've seen, I still hard screwed the ROM's in on the opposite side of the case to limit any possible vibrations (and resulting noise) that could result from not taking the time to do such a simple thing. Yes... I know... You can say it... It's pedantic... But I don't care.

Side Panel with Sound Dampening Material

Lian Li PCI Fan Controller Hard modified to be hard mounted to back of case, because top mount fan wires were not long enough to reach PCI Slots. 3 fans... 2 extensions... Forced to mod it. Online listings for this fan controller is wrong... It can control up to 4 fans... Not 3.

Modded Lian Li Fan controller from back side of case. (This Mod was done using a Drill and a Dremel... Damn I love my Dremel... Best Modding tool I ever bought.)

CPU Cooler

Aggravation... Hard to see, but if you look closely, you'll see I had to modify the motherboard in order to get the mounting bracket for the CPU cooler to sit properly... This part really pissed me off. Never fun... Always scary...

Lots of swearing!

Power Supply

Top Mounted fans from inside.. You'll see that the cutting for the sound dampening material for the top was not easy.

Tv Set up.. My Tv is actually a Fully 1080p HDMI Computer monitor with a Virgin V+ box and a DVD player for audio. V+, DVD, and Computer are all connected to an HDCP compatible HDMI switch box and then connected from switch box to the monitor via an HDMI Cable. Computer Digital Optical audio connected to back of DVD player. My PC is my Blu-Ray Player. It was either 300 pounds for a Blu-Ray Player, or 60 pounds for a Blu-Ray ROM... I'm not rich. ROM it is.

Entertainment Center Equipment from top box to bottom... HDMI Switch Box/DVD Player Receiver/Virgin V+ Tv Box
Also with this setup, if I play on my PC a game which uses an XBOX360 controller. I can easily switch the screens and play the game on the couch. Surpisingly, this has proven very useful when I have friends over. I love this setup. The new refit is quiter than my old case, cooler, and the couple hardware changes I made (including losing the RAID) has actually proven to improve my system performance by a considerable and noticable margin. And has improved overall system stability. One fair warning about this case. While the sound dampening material makes a considerable impact to the noise level of this case, I highly (and I do mean highly) recommend using a proper fan controller for the CPU heatsink. The motherboard CPU fan connection just wants to go full boar non stop, so even with dampening material, it was very loud. Once I rewired to the fan controller, this case is now dead silent. Even quieter than my old case and that's a big achievement. Especially considering how open this case is. I expected it to be louder. But the rewiring to the fan controller (I was experimenting for results) the CPU cooler keeps my CPU at a frosty 22C. So I'm very happy. What do you guys think?
On one final note. The reason I chose the fans I did, was not only because of their stats, but also because they have a significantly dimmer glow from most LED fans. While I do like lights on computers, I don't like seeing those lights glaring all over the place when I'm watching a movie or trying to sleep. These give enough glow to be seen and look cool, but not bright enough to light up the entire room in the dark. I'm very happy with the result I got from that choice.