Last week, I read a chapter out of Visualize This by Nathan Yau. I was, of course, delighted to see that he was championing the use of R. One really cool thing that I learned from his book, and was very surprised about, was that you can export an R graph in PDF form and then easily edit individual elements of the graph in Adobe Illustrator.
what? and spend oodles of $ with Illustrator just to make R graph look more spiffy in a publication? (read undisguised plug for open source) try Inkscape!
disclaimer: there's all sorts of good reasons to use Illustrator especially if you do design work, opensource projects make an easier entry into vector graphics editing for a cheap budget.