Hey noobe!
I just completed my build of a MicroFly with a C2D E6400. I used my Antec 430watt PSU (standard size), two optical drives, flopy drive, Audigy2ZS sound card, VIA Firewire card, BFG 6600GTOC AGP card, and 2x1GB PC3200 DDR DIMMs on an ASUStek P5PE-VM mobo. The case, while flimsy when not fully fastened together, is spacious and cool.
I am only using a Zalman Alcu-7700 heatsink and fan long with the PSU exhuast fan and idle at a mobo temp of `40c with the CPU at around 40c as well. Running at 2.13GHz, 1064MHz FSB under load it maintains around 50c for the CPU and is fairly quiet.
The mobo tray is ok, but is essential in this case as the frame interferes with the installation of the CPU heatsink/fan as well as the PCI cards. When pulling it out you have to disconnect ALL of the power and IDE cables to prevent snagging and bending their connectors. The interior edges are not rolled and are rough enough to cut you or wiring. I filed them smooth and used rubber tubing to mask some of the pass-thru channels in the frame. Not a biggie!
I wanted to keep cost down so elected to use the P5PE mobo in order to keep my existing components hile upgrading the CPU and not have to buy a new mobo, DDR2, PCIe cards, SATA HDDs/optical drive, and PCIe video card. I have had good experience with ASUS and since their are so few boards available the suit the bill with Intel being too expensive and not trusting VIA based mobos I stuck with ASUS. The boards manual backward in its depiction of the IDE Primary and Secondary connectors on the board which caused a problem, but in questioning myinstallation, I saw the conflict between the stencils on the mobo and hat was shaown in the manual.
Also, like the page for the Microfly on Ultra's website, the manual is severely lacking in information. However, for the price the MicroFly is an excellent case, IMO. I read one review that stated the author couldn't get a good fit and alignment of the side and top panels once the case was loaded, but mine looks great after having the tray in and out and replugged 4 times.
If I had the $$ I would have opted for a 975x mobo with all it requires, but still, this setup smokes compared to my P4 2.53GHz/533MHz FSB socket 478 rig.
Good luck on your build!