Hide Forgot
Before switching to gnome shell, I had xchat's: preferences->alerts->enable system tray icon enabled. One can then simply close the window, and use the icon to restore it (or click on the icon to hide it). The gnome-shell seems to stop showing the notification / tray icon as soon as the xchat window gets hidden, making it impossible to restore the window. I also tried clicking the xchat icon which I put in my favorites menu, but that predictably starts a new xchat instance. I understand that xchat does not fit well into the gnome-shell model, but at a minimum gnome-shell should not remove the tray icon from the notification area when then main window goes away, as the tray icon window does stay around (works with gnome2). Otherwise there is no way for the user in cases like this (note that there are other apps which will also hide their main window only showing a tray icon) to restore the main window of the app.
This is fixed in 2.91.93.
First of all thinks for the fix! I can confirm that this is fixed when using gnome-shell normally. However when you run "gnome-shell --replace", the xchat tray icon still disappears, even if the xchat main window is visible at the time of the --replace -> re-opening.
That's an xchat bug; it does the same thing if you just kill and restart gnome-panel under 2.x. For some reason, xchat does not properly handle having the notification area go away and then come back. (I tried to debug this at one point and couldn't figure out why, but it looked like xchat must have been doing some sort of low-level event filtering or event mask munging that was causing GtkTrayIcon to miss the PropertyNotify event telling it that a new notification area had appeared.)