[Brian]

OmniGraffle supports adding "Jump to another canvas" actions to shapes in the document, but if you mean an animated drop-down menu that functions like an app, not really. I have seen folks use Applescript to do some simple animations in OmniGraffle, but a clickable app mockup would be much more complex to try and script.

I think this falls into the "Technically possible, but unfeasible in day-to-day work" category. Folks do use OmniGraffle to mock up applications, but AFAIK the mockups tend to be static screenshots.