Comic Life is great for creating story flows in a rough and ready way, with a little style.
Balsamiq is an excellent tool for rapidly creating purposefully low-fi wireframe mockups
Napkee enables you to import Balsamiq mockups and turn them into HTML prototypes! Lovely!
Axure is excellent for rapidly creating interactive prototypes.
Liferay Portal is a pretty awesome portlet container that, with a bit of UX (HTML, CSS and JSP) hacking, enables you to rapidly produce fully functional portals. It comes with a vast array of portlets out of the box, saving you a whole load of time.
JQueryUI is a lovely toolkit for quickly developing interactive prototypes. I’m not completely convinced by it as a production tool (heavy JS? but i could be wrong), but excellent for prototyping