In regular OSX apps and in the main menu of Firefox the menus fade away when closing. Im not sure but they might fade in too, though if so it's much faster than they fade away. However XUL popup menus (bookmarks toolbar, context menus etc.) do not do this. Not a biggie but would be nice from a consistency point of view.
Tooltips and context menus faded away in Firefox 2. Was there a change in the popup implementation that broke the fading?
It was the switch to Cocoa. Bug 344570 added fading menus while we were still using Carbon but this code wasn't migrated. Moreover, it wasn't very flexible since it unconditionally applied fading to all popup windows and used the same settings for every popup type (e.g. tooltips faded with the same speed as menus).
I'm going to implement this in a cross-platform-available way in nsXULPopupManager.
Also, the app menu fades in, but doesn't fade out on the latest Aurora release.