So far, the only notification available is audible, which doesn't help if you were away from the machine a minute, the sound is off or, if X still inverts the menu bar, you were not looking at the screen that instant.
Some sort of visual notification would be nice. Maybe for new channel text, the icon's eyes could glow extra bright or something (just as a background hint), and animate or bounce the Dock icon for an incoming private message.
Stuff like this, though, could use being in a plugin, but we don't have an RFE list or category for plugin developers to read. Maybe we need to have two categories set up - Application, and Plug-ins, to settle this issue. Or maybe a separate list altogether (I did create http://telcontar.net/stdin/?topic=2 but that didn't go far ;)