Balsamiq's "Mockups" tool is ideal for throwing together the straw-man, discussion point, come... well mockup, for application development. It's the perfect "electronic napkin". Quick. Intuitive. And if you're a scribbler, doodler, or back of the envelope kinda guy then this is the perfect app.
Daemon is big on blueprints for application development. Annotated wireframes are a whole lot easier to share between stakeholders and developers than word docs with "thump factor". It's a big part of taming the client. Traditionally we use Visio for larger documents in house -- you know, the ones that keep pulp mills in business. And if I'm on the Mac I'll usually mock things up in Omnigraffle -- the Graffle is good with workflows.
But what I like most is the freedom of a good lead pencil -- I always have one about. The ideal mockup is something I can scratch out on a piece of paper and pass around. Beyond the visceral, a hand-drawn wireframe conveys a different vibe; by its very nature it's imperfect. You're not sweating the "look and feel", instead you're focused on the form and function. Recently I stumbled across Mockups from Balsamiq, a tool that just might be the digital pencil I'm after.
Mockups is the brainchild of Peldi -- one of the genii behind Macromedia Breeze (now Adobe Connect). Built entirely in Flex and deployed through AIR, Mockups for Desktop is a marvellous little cross-platform wireframing tool. It's one of those cute apps that's fun to play with and gets you hooked from the get-go.
You can download a trial (for Windows, OSX and Linux), minus save and export options, and give the software a good work out before you buy. Mockups for Desktop is a bargain at $79USD -- not to mention free for open source and non-profits -- and discounts are available for multiple user licenses.
Mockups is probably not suited for large scale documentation. The UI doesn't handle lots of related wireframes all that well (just yet) and your print options are limited. That said, your finished diagrams look fabulous and can be easily exported to PNG and embedded in email, word, or your document of choice.