Edit.Edit. Our new paper gives a close connection between monoid representation theory, poset topology and Leray numbers of simplicial complexes with classifying spaces of small categories thrown in. If browsing this paper doesn't convince you that monoid representation theory has something to it, then I don't know what will.
Edit. (2/18/14) Since this question just got bumped, let me add the new paper http://arxiv.org/abs/1401.4250 which gives a general introduction to Markov chains and semigroup representation theory and new examples.