Comment 15 for bug 393138

It's still an issue, but only if you're not using empathy with the indicator applet (for me). There's an option in the preferences, "Show incoming messages in the messaging menu", which if un-checked displays an empathy icon in the notification panel instead of the indicator applet.

If this is unchecked, then clicking the notification icon opens the empathy window (just like pidgin), but clicking it again doesn't close it and no other close action works either (eg, mod-shift-c from xmonad).

On the other hand, if this option is checked and the buddy list is opened from the indicator messaging menu then it can be closed as normal.