For reasons I don't begin to understand, its authors have written it as a Firefox plugin, but Pencil is a great FOSS prototyping tool. Like Balsamiq Mockups, it comes with a massive number of prefabricated components that allow you to quickly throw together a demo screen. Also like Balsamiq, you can have multiple pages in a sketch, and link between them, allowing your programmers and designers to "click" certain buttons, and get a feel for what should happen when that occurs.
Unlike Balsamiq, its default mock widget set looks like real widgets, which I get concerned causes programmers to slavishly imitate the mockup they see on screen. Thankfully, a sketch widget template has been distributed with Pencil for awhile now. Also unlike Balsamiq—and hopefully not surprising for a Firefox add-on—Pencil exports its sketches to HTML, not Flash/Flex.
I know Pencil looks weird because it's a Firefox extension, but it actually works very well, and is easy-to-use. I am not ideologically attached to FOSS and don't mind spending $80 for great software, so I'll be honest and say that I use Balsamiq over Pencil. I find Balsamiq's general workflow and ease-of-use superior to Pencil. But Pencil's still a great tool. If you're looking for a FOSS prototyper, I think you'd have a hard time doing better. Launch Firefox and go check it out.