Standard user modes are listed in help/opers/umode
Standard server notice masks are listed in help/opers/snomask
Standard channel modes are listed in help/opers/cmode

The sgml docs have more detailed descriptions.

User mode +x (hide hostname) is provided by contrib/ip_cloaking.so
Server notice mask +F (far connects) is provided by contrib/sno_farconnect.so
Information on the caller ID system can be found in doc/features/modeg.txt