This is something that's been thoroughly discussed on DN and for all your prototyping nerds this is nothing new. However I thought it would be useful to pull together relevant links and articles tying everything together. This is a high-level overview of the three most popular and granular prototyping tools.
I've been working on a tool called Mitya (www.mitya-app.com) to do exactly this - prototype interactions! It's a timeline based animation tool that exports to HTML5. The goal is to help designers build the prototypes visually and then export to an interactive format, so you can 'feel' what it's like.
It'll be a few months before release, but an early alpha version will be ready next month. Let me know if you'd be interested to take a look. I'd love to hear from more designers who are designing interactions.