I talked about how you can create prototype for mobile and web application, but the thing is you have to come up with the image (most likely using photoshop or other softwares to create those images and icons.) and it's not that easy. Not everyone is a designer and it's more than a designer it's a web designer. There are sites where you can use to wireframe different pages of your site and with web based application like invisionapp you can create a reasonable prototype without much of desiging skill (Just drag and drop). There are: WireFrame.cc, Moqups, and Pencil. What's interesting about Pencil is that it is a desktop application and not web page. All three are pretty much the same, I will be talking about pencil with invision in this post. Using pencil to create the layout images and icons and with invision to wire it together to create a prototype. Here is a example.

I know its pretty bad.

After working with Pencil for a few days I felt like it was limited as a tool for wireframe, then I discovery Justinmind prototyper. Justinmind is just like invisionapp but with their own built in wireframe desktop application that support more modern UI template for you to design. You can download the interaction wireframes application here.

Reminds me of photoshop, you can add layers, shape and changing color of the UI. Here is a demo of justinmind.com

There's a lot of drag and drop and changing position/color. Other than that there isn't much.