Web site development is mostly a complex process, often made more so by people from IT, marketing, publishing and design all having to sit in the same room together for long periods of time. Phrases like “content is king” and “monetising the clicks” run thick and fast. While some proceed according to “principles of information …
We're using OmniGraffle and Illustrator in our agency setting, depending on whose doing the layouts (developers like Omni, designers like Illustrator).
Something I've noticed picking up as a trend is to wireframe (or even design) directly into the browser, either hand-coding or using a tool like Dreamweaver (I know, I know...). The advantage is it lets you create a live mockup where links, layouts, etc display in a familiar interface. If done properly, the prototype can even serve as the base of the real layout.
Wireframes/prototypes are great for communicating with technical people, but for less technical clients prepare for a lot of "Why's my website all grey and boxy? What's all this greek text derp derp...". Solutions to that problem welcomed :)
I have found only one mockup program that is actually any good - Balsamiq Mockups (http://balsamiq.com/products/mockups). Multi-platform so you are not restricted to Windows and has some very nice features.
I actually use a combination of Balsamiq for wireframes (use with Napkeet o turn your wireframes into clickable prototypes) and Omnigraffle for the creation of site map diagrams.
There also some nice Web-based tools like Mockingbird. I' avoid Visio though, at least for Wireframes. You might as well use Powerpoint.
We use OmniGraffle for wireframes & high level site maps. I've tried online wireframe tools but have found it difficult to get clients to actually "sign off" online wireframes. They seem much more willing to physically sign off a printed pdf!
Nice advert for Visio...