Markdown is important for documentation, it is very nice to see README.md
can be automatically show in html format in github like https://github.com/twitter/bootstr
I use following post-receive hook in my remote repositories which are made browsable with gitweb.
#!/bin/sh
#
# Post-receive hook script which generates README.html to git-dir from
# README.md found at the head of master branch in repository.
#
# Gitweb can read the README.html and embed it to the project summary page.
git cat-file blob HEAD:README.md | markdown > $GIT_DIR/README.html
That script is run when I push commits from my local work repositories to the remote bare ones. You could use that or something similar depending on your workflow/setup.
More information about git hooks: http://book.git-scm.com/5_git_hooks.html