Paper, whiteboard, prototyping.
I also use a tool that nobody else has mentioned.
Once upon a time, I was put in charge of a development project that was going to cost on the order of $2-3M. The company had already lost about 10x that much on an earlier version of the project, which they were throwing away and starting over from scratch. Senior management was determined not to make that mistake again, and so from the start they wanted the design reviewed. So they got a very senior (and fabulously expensive) technical consultant from one of the most heavy-duty consulting firms in the world, and they paid an ungodly sum for him to spend three days going over the design with me. (Nerve-wracking? You bet!) I spent three days talking and drawing on the whiteboard, and he spent three days capturing everything in...PowerPoint.
But PowerPoint sucks, you say. Its drawing tools are primitive compared to Visio or Illustrator or practically anything else, you say. You can't make a drawing of any complexity. All true.
On the other hand:
It may seem a little tautological, but the main thing that using PowerPoint does for you is that it enables - and forces - you to construct your design documentation in a way that can be presented to other people.
It's not possible to draw a huge and complex drawing in PowerPoint. What you have to do instead is break things down into simple pieces and present those pieces and their interrelationships. It's very hard to make a drawing in PowerPoint with more than six or seven boxes, true, but on the other hand it's also very hard to understand a drawing with more than six or seven boxes.
Another thing that using PowerPoint lets you do is start with a simple drawing and gradually add complexity to it, explaining each addition of complexity on its own slide or set of slides.
Once you get good at that, you can also use it to make "animations" of the system you're designing, illustrating changes of state at each step in the process as you move from slide to slide. In essence, you can create a visual prototype of your design that other people can examine and step through.
I've found this immensely useful in communicating the behavior of interfaces between disparate applications to non-technical users of the individual applications. It made it possible for them to see how the changes I was proposing to the one application they understood were necessary to support its interoperation with the other applications. I could see these people going from confusion and disinterest to engagement and even enthusiasm as we walked through the process step by step. This has gotten me buy-in that I wouldn't have gotten otherwise. In more than one case, a non-technical person has taken a copy of the presentation home, played with it on his own time, and gotten back to me with questions and ideas that I really needed to hear.
(Another nice thing about this is that you end up making PowerPoint presentations that don't look like any PowerPoint presentation anyone else has ever seen. That alone keeps peoples' attention.)
It's certainly not the first tool that I reach for. In fact, I don't use it unless I really, really have to. Because PowerPoint is frustrating and awful to use. But haven't yet found myself leading a design review and thinking "man, I wish I hadn't used PowerPoint to do this."