I've used both.. I prefer the Dremel, it's cuts are just alot cleaner, and its alot easier to cut a radius with a dremel. It pains me to think back to cutting my first 80mm fan hole with a jigsaw, it was just disgusting when I was done. I use those fiber glass reinforced cutting wheels (and alot of them... for my big window which is about 1.5 feet by 1 foot I plan to go through at least 10 of those little guys. Maybe a combination of both would work best for you? At anyrate, have fun with your modding and be sure to post pics!
Tom