Get a fan grill and trace around it and mark the holes for the screw to mount is. I personnally use a drill to make the starter hole and 4 screw holes, then I cut out the fan hole with a fine toothed jig-saw. It works pretty fast. Sand or file the edges and install the fan. I've done about 10 this way and they all worked pretty good. I've also cut out for window kits and done some hacking on old AT cased with that same jig saw. Best $25 I ever spent.
Dude!!! Buy yourself a $10 nibblier. It's a hand tool that cuts by "nibbling" little by little. Takes alot of time but cuts BEAUTIFULLY!!! 90 degree and circular cuts are no problem for the Nibblier. Only down side is that you have to drill a start hole but that's no problem w/ a drill.
The hole saw is for cutting large round holes for things like door handles in wooden doors. They are kind of expensive and require a hefty drill. I use the jig-saw because I have one and I use it for many things. I also have the drill, but it is a small one and has trouble just cutting 2" circle, let alone 3 1/2" circles.
Here is a picture of one:
The largest they had where I found this picture was 2-3/8" and it cost $10 + shipping. Most kits I've seen only go to about 2 1/2".
I did find this place with hole saws up to 6". The 3.5" hole saw was only $9.11, but the arbor that attaches the blade to the saw was another $10.99.
Fine toothed metal cutting jig-saw blades are only $1-2. If you were building lots of cases and needed to cute many holes, then the hole saw would be the best idea. It makes very nice holes.
I used my dremel and a CAD template to make perfect octagonal holes- cut out on the lines, score, and fold back. Edges are clean and not sharp like you get from a drill or nibbler, and it looks very professional
...Or if you're like me, you take all this effork to make the holes look nice and perty, only to discover you can't fit the fans inside the case and have to mount them outside, completely defeating the porpose. DOH!