All-purpose: Dremel with fiber-reinforced metal cutting attachment. Dremels will technically work for anything, but they tend to create a more ragged edge and mess up the paint in the area more than other stuff.
Straight cuts, some curves: Jigsaw with fine-toothed metal-cutting blade. I haven't had much luck with this personally but I probably just have a bad jigsaw, or I'm not doing it right. Or both. Other people recommend this highly though.
Circular holes (for fans usually): Hole saw, haven't used it personally but I'm sure it's the best solution for this.
Straight cuts: Skilsaw/circular saw with metal-cutting blade. These are supposed to be the very best for a straight cut, and should provide a very clean, straight edge.
I plan on placing a fan at the bottom of my case as an intake. I'm going to install a filter and postion the fan so that it blows directly into my 8800. Depending on if I figure I need it, I may also install a exaust at the top of my case.
If it's on the bottom of the case, appearance probably doesn't matter as much as functionality... so I'd just use a Dremel. They're easy to use and you may find more use from one in the future than from another tool.
One thing I'd like to note is that you should make sure that the bottom of your case is raised up a centimeter or two off the ground so that the air can get into your bottom intake, or the fan will be useless. (You may need to buy new case feet to accomplish this).