I also have this bug. 
I use KAlarm and my computer with Ubuntu 12.04 (Gnome desktop) took several 
minutes to shutdown.

Link http://ubuntuforums.org/showthread.php?t=1764048 gave me the hint how to 
solve this problem. This link contains methods to prevent te starting up of 
nepomuk and akonadi in 3 steps. 
If you don't want to use KAlarm, it might be safe to apply all three steps. 
However, doing so, KAlarm could not be used. It asked to start-up akonadi 
first. So I tried what would happen if I only used the two steps preventing the 
(complete) start-up of nepomuk, and that worked great. KAlarm works and Ubuntu 
12.04 shuts down within a few seconds. The steps to apply are:

1. Add the following lines to ~/.kde/share/config/nepomukserverrc (and
their sections if they don't exist) (change the value from "true" to
"false" if they do exist and are set on "true";

[Basic Settings]
Start Nepomuk=false

[Service-nepomukmigration1]
autostart=false

[Service-nepomukstrigiservice]
autostart=false

2. Remove the file /usr/share/autostart/nepomukcontroller.desktop, if it
exists.

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https://bugs.launchpad.net/bugs/1053783

Title:
  Ubuntu 12.04 - Stalled shutdown after having had KAlarm opened; with
  package info.

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