I've noticed that I constantly get notifications about instant messages, 
e-mails, and the like.  I've also noticed that Thunderbird uses its own 
notification system, which seems to work much better than the one used 
by Pidgin et al.

The difference in these two systems is pretty simple and easy to compare.

When I get a notification about, for example, a new Instant Message, I 
get a black box in the top-right of my screen.  Hovering the cursor over 
this box makes it fade to transparent; clicks pass through, although the 
elements beneath the box are a little hard to see.

When Thunderbird notifies me about an e-mail, I get a box in the 
bottom-right with a list of new e-mail messages.  Clicking a message 
takes me to the desktop that Thunderbird is on and selects that e-mail, 
so it's previewed in the preview pane.

The latter behavior seems vastly superior to me.  I can't click an IM 
notification and be taken to the desktop with Pidgin on it and have that 
window brought forward and the appropriate tab selected; instead I need 
to recall mentally where all that is, switch desktops, switch to the 
appropriate window, and select the correct tab.  In this way, the 
notifications are effectively useless; they don't tie back to the source 
of the notification.

Most notifications I get are a pointless annoyance because of this, 
whereas they'd otherwise be helpful; I choose to ignore the event in 
question because it's too much work to respond to it.  The ones that ARE 
helpful direct me to perform a number of tasks to respond to them, 
rather than giving me something to click to follow back to the 
appropriate window.

I'm not sure why, but having a "notification queue" that lists all 
notifications you didn't respond to or dismiss seems useless.  It would 
be unbelievably cluttered; but I mean the very idea of checking 
notifications for stuff like instant messages that came while you were 
AFK just seems pointless.  Maybe the usefulness here is in reflexive 
response to events happening in real-time, rather than simply in 
response at all.

All I can really say for sure is that Pidgin giving me notifications for 
IMs that I can't click on to follow back irritates the hell out of me.

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