General comments on protocol design, and good reference material on a few protocols (especially mail-related; also ftp, time, and misc) by Dan Bernstein.
Hosts a copy of this open source search engine software for FTP servers. Knowledge about perl, ANSI C and shell scripts is required when installing it.
The end2end-interest mailing list is an active forum for discussing end-to-end Internet protocols (mainly TCP and UDP and related application protocols).