Chime in brothers and sisters!
Re: Prototyping an app
I've been prototyping using various means over the last few years.
IMO: There's nothing that beats the ease of use and efficiency of a pencil and paper to get the initial ideas out quick.
There are multiple options to prototype in the browser as well as native apps.
Omnigraffle is an incredible tool, but it's available only for mac. Adobe Fireworks is a worthy alternative for windows. Both of these tools have smooth learning curves, even if you are'nt familiar with them, you'll be able to grasp and use them in no time. For browse based tools - try balasmiq.
here's a good link that reveals the prototyping process at google/ideo.
designstaff.org
others:
onextrapixel.com
I'd also second Omnigraffle, and along with stencils available at graffletopia.com its quite irrepressible.
However If we are talking about web applications, then i'd say one could directly jump to HTML/CSS after having quick wire-framing with pen/paper.
Various well documented frameworks like twitter.github.com and foundation.zurb.com have made the process even more quick and simple.
