I'm a big fan of markdown syntax. I'm using it right now as I write this post via Movable Type Open Source, I use it with ikiwiki, and believe it or not, I also use it when writing letters and business documents. Markdown2pdf makes it even better.
However I do have one problem. There is a clash between the file naming convention I'm used to and the way italics is activated within Markdown.
I've written before about the importance of hyphens and underscores to programmers. In an obscure way, this is similar to the situation with ampersands (&) and XML.
I never understood why the ampersand was chosen as an entity token. Perhaps the writers of the specification didn't know how incredibly common a punctuation mark it is.
Like the ampersand in XML, I'm under the impression that its not a trivial task to globally alter the syntax parser of Markdown. Maybe its time to consider an alternative?