Alex van der Peet (of the OpenCog Hong Kong team) has been working on cataloguing all Atom types currently in use in the OpenCog code on the wiki site.
This page lists them all, with a page for each one:
http://wiki.opencog.org/w/Category:Atom_Types
A few of the pages still don’t have any information on them.
To all OpenCog developers: If you’re working heavily with a certain set of Atom types, please check out the corresponding wiki page, and think about adding some comments or examples.