Using the classname's part as path elements makes ugly paths:

ezcMailParserSet        => Mail/parser/set.php,
ezcMailSmtpTransport    => Mail/smtp/transport.php,
ezcMailTransportOptions => Mail/transport/options.php,
ezcMailAddress          => Mail/mail/address.php,

More logical names (mail_autoload.php):

ezcMailParserSet        => Mail/parser/interfaces/parser_set.php,
ezcMailSmtpTransport    => Mail/transports/smtp/transport_smtp.php,
ezcMailTransportOptions => Mail/options/transport_options.php,
ezcMailAddress          => Mail/structs/mail_address.php,


Some problems: