I cut out the T part in the bottom and bondo'd in some plexi to make it totally flat on the bottom (and even on the sides too). I'm going to paint the system a nice white/cream color. I cut out the inside part of the air vents on top, for increased airflow. I'll be painting a piece of screen the system's color and putting it on the inside to hide the holes better. I'll add two or three 1.5in fans at that opening.
I'm getting a pico-psu. Look it up, they're nice and small and only require an external DC power source. Most Pico-psu's come with the DC source for them. I'm using a simple DVD burner for media. The length is small enough to mount to the inside-top of the case, and it'll push the NES cartridge door open (with a bit of plastic inside the cartridge door). I opened the drive and soldered wires to the tact switch that normally opens the drive door, and attached them to the reset switch, so the reset switch opens the DVD drive. The power button will be the NES PC's powerbutton.
The board I have is an Intel Atom 1.6GHz Dual Core Mini-ITX. I have a 2GB stick of RAM, and it runs Windows 7 beautifully. I'm going to get a slim PCI video card for it as well. It's a really great board for $65. The tallest part of the board are the I/O ports on the back, about 1.25in tall (the CPU heatsink is only about an inch tall). It can emulate N64 really really really well. It surprised me!
For the ports on the front, I'm going to make an adapter that plugs into the original NES plug that will give 2 USB ports per controller plug.
Hope this may have inspired some things!