A couple of publications are in process that should help answer this question. The first is the _Blackwell Companion to Digital Humanities_, edited by Susan Schreibman, Ray Siemens and John Unsworth, to be published in Nov 2004: http://www.blackwellpublishing.com/book.asp?ref=1405103213&site=1 (Unfortunately, this one will cost about $150, but perhaps you can convince your library to purchase it.)
Julia Flanders, as part of an NEH grant, is editing a guide to encoding early printed books, with plans to include plenty of good advice about encoding in general. Preliminary report at: http://dev.stg.brown.edu/projects/wwpneh/.
Perry Willett University of Michigan pwillett@umich.edu