I've tried GutenMark (and gut.pl) and the results are decent but too much hand-editing afterwards. The ManyBooks editions do a good job of Table of Contents but they don't do any typographic cleanup (dashes, ellipses, quotes, etc.)
I've been playing around with the list I've got above and eventually I'm going to update it (things like escaping '&' must occur before anything else). The process will always require human intervention (simply because each Gutenberg transcription was by a person) and an important part of the process is learning the original transcriber's style.
Two items that help, a reference on the MobileRead wiki to
for layout control and Google Books archive of scanned books (for checking the original layout and typography).