Wireframes are used to show:
Structure - How will the pieces of this site be put together?
Content - What will be displayed on the site?
Informational hierarchy - How is this information organized and displayed?
Functionality - How will this interface work?
Behavior - How does it interact with the user? And how does it behave?
I draw wireframes using a pen and paper for initial testing. I then move to Abobe Illustrator (and Indesign) to create interactive flash and pdf files for testing and discussion. Click here to download samples.