One of the big programs used is called Art Pro. Took me a bit to remember but what it does is compensates the art for distortions. This makes the prepress very brainless considering the plate bounce, stretch and all the other nasty stuff that goes on in the flexo world.
Occasionally I have to distort art but that is usually for tapered mugs that use printed inserts, For the most part that can be achieved using envelope distortions, I use Canvas for most of the tough stuff, Illustrator, Photoshop and Quark for the rest.
If you do tons of vector work like I do, check out Canvas. Much of my work is fixing other peoples Illustrator CS files