What is the recommended software for drawing data structures such as graphs and trees?
The MO thread Per links to is pretty good, and this thread on tex.SE is also handy. The main tools that I've used:


TIkz/PGF
Ipe
Inkscape/Illustrator


I know that Mac folks swear by Omnigraffle, but I have zero experience with it myself. The main criteria for me are:


Generating PDF
Integrating LaTeX (with source styles for bonus points)
Being able to do color/shading etc easily. (Ipe 7 fails on that count)