How to restore missing app icons in Dock
I just had this issue and found the solution, so I wanted to share it.
I used CleanMyMac 2, which has never given me issues before, and lost some app icons in my dock.
All you need to do to restore missing dock icons is open up Terminal and copy and paste this:
killall Dock
My icons all returned instantly.
It's the easiest solution out there. And remember to run Permissions Repair with Disk Utility in case anything else got messed up.
OS X Mavericks (10.9.2)