There are 32 bits of folder flags. Most of the flags tell you what kind of server it belongs to (IMAP/LOCAL/News), whether it's a "special" folder (INBOX, Drafts/Sent/Template), and some miscellaneous attributes (e.g., is it configured for offline use?).
One perhaps surprising attribute is MSG_FOLDER_FLAG_VIRTUAL, which indicates the folder is a saved search. If you have a saved search in an IMAP account, it will be of class nsImapMailFolder, but have the MSG_FOLDER_FLAG_VIRTUAL flag set. The saved search can search over folders of different accounts and types, and in theory, it doesn't even have to search over any IMAP folders.
Another flag to note is MSG_FOLDER_FLAG_ELIDED, which says whether a parent folder is collapsed or not. This should be view, not model information, like the other flags, but our use of RDF for the folder pane introduced this anomaly. Getting rid of RDF in the folder pane would fix this.