The author has helpfully broken down prototyping software into 2 kinds:
Layer-based Tools (e.g. proto.io, Pixate, Axure, UXPin)
Code-based Tools (e.g. Quartz Composer + Origami, Framer.js)
I mostly use layer-based tools. I used Axure extensively for a while, then I tried our UXPin, and then I tried out Pixate, but the one I've mostly been using these days is proto.io.
One thing I really liked about proto.io is that I can create a custom screen size and skin it with some of their presets. This really came in handy since I'm currently working on a piece of software that is going to be used on a relatively uncommon device (the Getac F110). Proto.io's flexibility in prototyping for ANY device is key for me. (That's the main reason I gave up on Pixate -- I need prototypes for lots of devices, not just mobile apps!)
Also, the prototypes that you end up with are faster, work more smoothly, and look nicer than the prototypes you get with some of the other options (like Axure and UXPin).
