I wrote a Jekyll plugin that enables Pygments syntax highlighting for Kramdown-parsed fenced code blocks. It is heavily based on krampygs, but refactored to make it work with Jekyll 2.*.

In the standard setup, Jekyll Kramdown only works with Pygments for syntax highlighting when you use Liquid tags. This plugin makes Kramdown also use Pygments when using fenced code blocks. That way you can use more Markdown and less Liquid. Yay!

With this plugin enabled and Kramdown set to accept Github Flavored Markdown, your blog will parse and render markdown like you are used to from GitHub.

Check it out here: https://github.com/mvdbos/kramdown-with-pygments