Reinstalled gtk+, deleted ~/.gtkrc-2.0-kde4, and run equo deptest/libtest: everything sane. Problem was not solved.
But I noticed that I could start the relevant gnome-apps when starting it from command-line after I executed
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So I created a new user-account and voila everything runs just fine. But not in my old account. Same issue with the account of my wife.
We use these accounts since Sabayon 3.0, so it seems there's something in it , that's not compatible anymore after the last gnome-updates the past weeks. Last thing I did was deleting ".gconf, .gconfd, .gnome and .gnome2". Brought no success.
So I created two new accounts, moved the data over to it and deleted the old ones.
Thanks for the help!
Now everything is solved and runs perfect again!