I have added a section to http://notmuchmail.org/emacstips/
that tries to describe the common workflow of notmuch.el users. It is
not finished yet, and it might better belong on a page of it's own.

I also recognize that it probably overlaps with James' new page on
initial tagging somewhat, but I was thinking of a kind of gentle
tutorial that links to specific FAQ entries, mail threads and pages for
deeper discussions of specific issues. Corrections, additions, feedback (and
deletions) welcome.

Sebastian