As some one who has modded a custom side window before hand - A Drill, a good quality jigsaw with a proper 2mm aluminimum cutting blade (was for a Lian-Li case), and then some hand files for making sure the cut edges are smooth.
A proper perspex drill bit and some nut/bolt fixings for the actual window.
And lastly, a proper workbench/g-clamps for holding your panel as you work!
Make sure you use some masking tape to cover the surface that your cutting on, and that you draw your cut out accurately.
A steady hand is all you need - just remember its not a race, take your time, and cut as straight as possible. The files can then be used to smooth down the cuts and the finish off the corners.
Jigsaws work best by having two straight cuts meet, rather than trying to cut round a corner in one motion.
Its actually a lot simpler than all this, and I intend to mod a window into my current Lian Li A70B case - keep an eye on the Project: AirRAID thread here in Case Central.