You can buy window kits for PC cases, which are basically a template you cut to size in the PC case, and a perspex windows and a some stuff to fix it in with. There's plenty of places on the net to tell you how to put in windows.
I quite like Window mods, but there's only any point in having them if you have a pretty heatsink and mobo, and light the inside up with cold cathode tubes (two is good - a green at the bottom and a yellow running up the left hand side is my fave configuration). For this reason, I think that the windows should be perfectly clear, not tinted blue or whatever. I'd go for the clear full window side panel personally; chuck in a Thermaltake heatsink and soem cold cathodes and you have th sexiest looking computer in the world.
Speaking of which, we've decided to use this case for the computer my flatmate and I are going to build (well, it's going to be his computer, but we've been doing the researh together).
Spec so far:
Lian-Li PC 60 case with windowed side panel and blowhole (it was a bitch trying to find a UK distributor for this, let me tell you!)
(also some Lian Li self adhesive labels to make the CD and floppy drives silver to blend with the case)
Gigabyte GA-7VRXP mobo - 8 IDE evices, dual BIOS, IDE RAID, ethernet, USB 2
Athlon 1.1 GHz CPU
GeForce 2 GTS
EG365AX-VE power supply
Thermaltake Mini Super Orb heatsink
256 MB Crucial DDR RAM
Pioneer DVD ROM drive
Twin Seagate Barracuda 60 GB hard drives
It's going to be the first home I ever see that runs nothing but Linux...