I've been thinking this ever since the enc modules first showed up in svn.
Since the old md5 implementation is broken, it would be nice to be able to convert to the newer md5 module (or even sha1).
NOW, obviously you can't just convert them, so what i was thinking is, a new directive in the conf file, something like EncConvFrom where you would specify the hash type you want to convert from (for example, enc_old) and in EncModule you would specify the new module (for example, enc_md5)
then, when the users identified, it would first check the password against the EncModule if it is incorrect, then check with the EncConvFrom module, and if correct, regenerate the hash with EncModule and update it in the database.
While this won't likely get many channel passwords converted, with would most definetly get all nickname password hashes converted within the nick expire time.
Although this might seem a little messy using 2 types of password hashes at once, it would definetly be a big help for security with people who have been using the old md5 method for a long time.