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 :)