I concur -- do any of the markdown environments listed above accept imported .cls latex style files? Would they even be compatible?

It seems like this would be essential for writing research papers according to a conference's template. If so, I would definitely use....

When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates).

You could modify the default template to use whatever style file you want.

Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.

Exactly. I've been using raw markdown processed with Pandoc as my sole document-creation tool for the past 3 years and it's worked excellently so far. Pandoc's pretty awesome.