With dovecot, they go into a couple of different directories. This is problematic because we often need to convert the form field data to csv values so it can be imported into a spreadsheet. So a professor can create an on-line form and end up with the data from it in an Excell spreadsheet. Slick (when it works). [...]
Alternatively, if you'd like to do it all in a batch, the format you are now using (with each message in a separate folder) is called "maildir", rather than "mbox". There are tools to convert from one to the other. Or, you can use a Perl script and use the tools from the Mail-Box distribution of Perl modules. These modules can read LOTS of different formats. See http://search.cpan.org/~markov/Mail-Box-2.068/ .
As it turns out, the script I wrote for the old mail server *almost* worked on the new server with dovecot maildir folders. I just had a mistake in the way it processed the message date. That made it appear as if the script would open the folder but not process the messages. When I rewrote that code to be more portable, it worked.
I don't know if this is of interest to anybody but here is a link to the perl script: http://www.math.wisc.edu/~jheim/stuff//mbox2csv
I believe that will work with formmail.php from sourceforge: http://freshmeat.net/projects/formmail.php/