Licq is a multi-threaded ICQ (originally; now it supports AOL and MSN as well) clone written mostly in C++. It uses an extensive plugin system to manage many different functions.
Dzen is a general purpose messaging, notification and menuing program for X11. It was desigend to be scriptable in any language and integrate well with window managers like dwm, wmii and xmonad though it will work with any windowmanger.