The PDF reader is more of a curiosity than an actual feature. Do not buy a non-DX Kindle with the intention of reading PDFs, I assure you that you'll be bitterly disappointed.
Some publishers offer native Kindle versions of programming books, like these:
http://oreilly.com/ebooks/
http://www.pragprog.com/titles
Both offer DRM-free ebooks, and you can download both the Kindle version and the full-size PDF.