I use pen and paper, together with a simple spreadsheet for calculating the gravity contributions of different malts. Weight times PPG times efficiency divided by volume. I love that equation. If I'm not sitting in front of a computer, a pocket calculator works just as well as a spreadsheet. It's also perfect for calculating ABV.
The only real brewing programs I use are Mr. Malty for yeast, Hopularity for iPhone for IBUs, and sometimes an online beer color calculator. Brewed By Us, I think?
I like piecing the elements of a recipe together myself, and doing at least some of the math in my head. I could be wrong, but I think this approach has made me a more knowledgable and careful brewer.