[ubuntu] Can't run commands outside of the terminal like logout, restart and launching video

I broke something in Ubuntu that is causing problems with launching applications and commands. I can no longer logout or shutdown from anywhere but the terminal. (Actually I've only tried shutdown and reboot from the terminal because I can't figure out what command will log out from the terminal in 15.10.) Also, some of my applications will not launch except from the terminal. Sometimes after a reboot I can get one of them to launch once, but if I close the application and try to launch again, then it will not work. The appplications which will not launch are video programs SMplayer2 and VLC, but not the Ubuntu default video player. That video player launches just fine. Also, the Calibre e-reader program does not launch outside of the terminal. I also caot open any video files or e-reader files by double-clicking or right click/selecting, with the exception of video files using Ubuntu's default video program.

Prior to noticing these problem, I was having a problem with my keyboard media key/shortcuts not working. While researching that issue I tried the fixes suggested in this bug report. Neither the Cairo Dock nor the gnome3 solutions worked, and shortly after that I began to notice the problems with logout, shutdown and launching apps. I still can't get media keys to work either. I think the gnome3 solution was probably a really bad idea and I tried to revert that but still the problems persist. Can anyone give me any idea what is causing all of this?