You can use a program like Morphine (not Morpheus, people!) to somewhat encrypt an exe. I've heard the absolute best way to do it, however, is to use
Armadillo. Apparently even those in the AV business claim that they just can't keep up with the changes that are made to the executable with this application.
There's a free trial on it too, which makes it nice. My guess is that it only works for so long, however.