I've just started a series of articles on my blog on this very subject! I'm starting by covering what the different types of quilting are, and then some ideas on how to narrow down what to choose.
I've been machine quilting professionally for over 10 years now, and I still get stumped at times. And other times, as soon as the quilt comes in the door, I know exactly what I'm going to do.
It does get easier the more you do it and the more you look at different quilts - online, in magazines & books, at quilt shows, etc.
Andi