Some time ago I mentioned the DAG (directed acyclical graph) primer by Judea Pearl et al. As noted in Pearl's recent blog post, a manual will be available with software solutions based on a DAGitty R package. See http://dagitty.net/primer/.
More generally -- that is, quite apart from the Pearl et al. primer -- check out DAGity at http://dagitty.net. Click on "launch" and play around for a few minutes. Very cool.