I just added syntax highlighting to my blog by wedging a call to Pygments into my fork of PHP Markdown Extra (yet another abuse of Michel's code). You could do a similar thing with MultiMarkdown by changing the _DoCodeBlocks function.
My fork of PHP Markdown Extra is here: https://github.com/drdrang/php-markdown-extra-math The syntax highlighting is in the "pygments" branch. A brief description of how I use it is here: http://www.leancrew.com/all-this/2010/12/syntax-highlighting/
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