Messaging Menu missing after upgrade to 12.10
Solution 1:
The way applications interact with the messaging menu was changed in 12.10, and not all applications have been updated. Pidgin (as of 20th Oct 2012) has not been updated. There is a ticket tracking what applications have been migrated. Until then Empathy could be used as an replacement.
Solution 2:
The messaging menu (normally in the top right) is turned off by default in 12.10. Simply open the "Broadcast preferences" application and check "Start service at login" to get it back.
in 12.10 Pidgin has been replaced with Empathy, so you may have to set it up.
Solution 3:
There's a patch available for pidgin-libnotify on a ppa here.
To add it, open a terminal and enter the following:
sudo add-apt-repository ppa:jconti/gnome3
After you've entered your password, press enter and observe that the signing key matches 6E3AB2D3. Then update and install the patched package:
sudo apt-get update
sudo apt-get install pidgin-libnotify
If all went well when you start pidgin you should see notifications in the messaging menu.