A post in Miguel’s blog mentions a system called Gnome Notifier, which provides a way for applications to use area in the panel to get the users attention rather than using popups. I thought that XChat used to have a panel component that would tell you what tabs had activity, so that you could switch to another desktop and know when to switch back (without having to turn sound on… ugh, I hate notification sounds). But I can’t find the options on my Fedora system, so maybe I just imagined that. I would love to see notifications go to the panel instead of popups.