I've used a ton of these tools (two of my favorites are balsamiq and wireframe.cc) and am always excited to check a new one out. That said, at least half of the time, I end up going back to my plain old graph paper notebook and pen.

It just feels more natural, and I find that due to that I usually end up getting more designs and ideas fleshed out more quickly, which is really what I'm going for when just starting a project and getting some wireframes down.

Overall, I tend to use wireframe "tools" when working with a other team members or clients (or in any other situation where passing a notebook around isn't feasible), and go back to pen and notebook when working on personal projects or just want to quickly map out an idea.