This is a list of the most common desktop tools used for Rapid Prototyping software and interaction. You might also want to check out the comparison table.

• Balsamiq Mockups: This relatively inexpensive ($79) tool is fantastic, and for student use there is a free 30-day trial. Balsamiq allows you to create really great wireframes that have an awesome, hand-sketched look to them. You can import your own images, and export your screens in a variety of formats. Best of all, you can also link your different frames together and then test them out in full-screen presentation mode. Balsamiq comes withs a bunch of built in widgets for desktop apps as well as devices such as the iPhone. There is also a large community of users sharing extensions, and building software that wil translate Balsamiq bmml files into other formats, such as HTML/CSS web pages, to iOS and Android and even to Flash. I definitely teach this tool to my students.
• Cacoo: This is an online diagramming tool that allows for the creation of wireframes, and fully supports collaboration. There is even a version that works inside Google Hangouts, so that you can hangout with others in Google+ and work together on a wireframe. A free account allows you to create 25 sheets/pages, and allows you to export as PNG. Upgraded plans include versioning, unlimited sheets and exporting of files to  SVG, PDF and PPT. You can buy stencils to help jump-start your diagrams, and you can use the chat window to talk to your diagram collaborators. Wireframing features include a rich library of web, desktop and mobile widgets, excellent, direct manipulation formatting interface, and the ability to import images. There is no interaction here though – no ability to create links between frames, and the wireframes themselves are completely static images.
• Axure RP: Axure is a full-featured prototyping app that works on both Windows and Mac. This is a pricey program that costs about $600, though there is a 30-day free trial. Axure is full-featured and allows you to build nice web and mobile app prototypes. It exports to HTML, allowing you to actually create basic web apps that work. It also creates software requirements documentation for you automatically, with screenshots. There are a number of widget libraries that can be imported, however, note that these are pictures of widgets, not working widgets, as is usually the case with prototyping tools.
• Flowella:Flowella is a free app from Nokia that allows you to import screen images and create simulations of interactions built on templates of Nokia phones. You can set up what happens when people click on various parts of the interface, when they press hard buttons on the phone, when they shake the phone, etc. This is a somewhat limited app, and is obviously tailored to Nokia products, but it’s free and works reasonably well for prototyping mobile stuff.
• Prototyper Free & Pro: Both Windows and Mac versions available. The pro version is in the $500 price range. The free version seems to work fairly well, though. You can also try out the pro version with a 30-day free trial. When you start creating a new prototype in Prototyper Free, you are asked whether it is going to be an Android  320px, Android Tablet, iPhone, iPad, web, etc. prototype, and then it sets things up for you so you get started fast! However, Prototyper Free does not allow you to add any interactions, or even linkages between screens. Prototyper Pro allows extensive rich interactions, and a fuller widget library, as well as developer notes, the use of variables, templates, etc. Prototyper Pro also allows you to build different scenarios for a single prototype, which are basically like chauffeured explorations of the prototype. Finally, prototyper allows you to specify actions and screen transitions based on standard touch gestures, device orientation chagnes, mouse and keyboard input. Prototyper Pro also allows you to import data from a CSV file and has an extensive Data Master system for making use of that data in various datagrid type widgets. There are numerous widget libraries that can be imported, though in the free version the widgets are just pictures, not active. There is also an online prototype sharing system that allows you to collaborate and get feedback on the prototype.
• Microsoft SketchFlow: This is part of Microsoft’s Expression Studio, the development suite for creating Silverlight applications. As it is a Windows-only application, I have not used it.
• FlairBuilder: This application is available for Windows and Mac, and costs about $100. There is a free two-week trial version available. FlairBuilder is designed for prototyping and wireframing websites and Internet apps, but also has some widgets for Mobile. It allows importing Balsamiq bmml files. The level of interactiveiy in FlairBuilder is impressive for a tool that costs $99. It does not allow import of data files the way Prototyper Pro does, but most widgets are interactive, and there are conditionals, variables, delays, and other fine-grained interactivity controls. There are two styles: plain and sketchy, but the sketchy style isn’t as nice as Balsamiq’s.
• Mockups.me: This application is very similar to Balsamiq Mockups, and even imports the bmml files from Balsamiq. There is a reasonable set of widget controls, but there aren’t really any extra libraries of widgets to use. One annoyance is the lack of scroll bars to move around the prototyping canvas. Movement around the canvas requires an explicit mode-switch to the hand tool, or explicit zooming in and out using the +/- tools.