Markdown2 fenced blocks and Pygments. Out of the I box I just couldn't get it work. So I don't use fenced blocks and hacked my own solution.

md2-pygments.py

from lxml.html import tostring, fromstring, html5parser
from pygments import highlight
from pygments.formatters import HtmlFormatter
from pygments.lexers import guess_lexer, get_lexer_by_name
from pygments.filters import VisibleWhitespaceFilter
# hack hack ...
# ignore code contained in pre. I just want the text in the pre
def flatten(elem, include_tail=0):
    text = elem.text or ""
    for e in elem:
        text += flatten(e, 1)
    if include_tail and elem.tail: text += elem.tail
    return text
# hack hack ...
eDiv = fromstring( '<div xmlns="http://www.w3.org/1999/xhtml" >' + html + '</div>', parser=parser)
formatter = HtmlFormatter(lineseparator="<br/>",cssclass='codehilite')
for element in eDiv.iter("pre"):
    language = ''
    mdPre = ''
    element.text = flatten(element); del element[:]
    match=re.search(r'^(\w+)\s', element.text)
    if match:
        language +=  match.group(1)
    try:
        lexer = get_lexer_by_name(language, tabsize="1", stripnl=True, encoding='UTF-8')
        mdPre += re.sub(r'^\w+', '', element.text)
    except ValueError, e:
        try:
            # Guess a lexer by the contents of the block.
            mdPre += element.text
            lexer = guess_lexer(mdPre)
        except ValueError, e:
            # Just make it plain text.
            language = 'text'
            mdPre += element.text
            lexer = get_lexer_by_name(language, tabsize="1", stripnl=True, encoding='UTF-8')

    lexer.add_filter(VisibleWhitespaceFilter(spaces=True, newlines=True, tabs=True, wstokentype=True ))
    pygmented = fromstring(highlight(mdPre, lexer, formatter))
    element.getparent().replace(element, pygmented)