On Wed, Jan 14, 2015 at 12:22 PM, Marcel Oliver <m.oliver@jacobs-university.de> wrote:
Some of the main culprints for me are nemo, evince, and okular;

The applications that you mention are parts of specific desktop environments. The messages that you see are not meant to be visible to the user, unless something breaks; in such a case, such programs would pop up a warning/info/error window, notifying the user about the problem. Messages about missing themes or services that belong to the parent DE, but which are not essential to the core functionality of the programs, do not (usually) fall under that category, given that they don't stop the programs from working and in most cases they are logged somewhere (e.g. in .xsession-errors or journald).

On the other hand, if every message that was not meant for the user were suppressed, it would be very difficult to troubleshoot such a program, should an actual bug come along, because you would need a different build to get useful output in the console or a logging service.

So, your options are to learn to live with the output of these programs, redirect it to the null device, start them from their launchers or via the command prompt (Alt+F2).