If I understand you correctly, you maybe referring to multiple entries for the same program.
Evince would be a good example because it is common to Lubuntu, Ubuntu and Xubuntu.
What you could do is to go into
/usr/share/applications and hunt down "common" .desktop files.
Sudo edit the "Name" lines to make them distinct if you wish or add
NoDisplay=True to the end of whichever .desktop file you don't wish to see as an entry.
Based on your comment, it appears that if you're using KDE (for example, since you mentioned Konqueror in the comment), you don't want to see Firefox or Chromium in KDE menus.
There are two possible entries you can add to the relevant .desktop file. Use:
to prevent an app from being seen in a specific desktop environment, KDE, in this case.
Or, you could go the other way and add
to restrict an app's visibility to a specific desktop environment, XFCE or Unity, for example..
In any case, do look at http://standards.freedesktop.org/desktop-entry-spec/latest/ for detailed information.
Just to be clear, I don't know of any way to do what you want automatically without the hassle of sudo editing each file.