I have the same problem with my Retina MBP (the 2.3 GHz model); after upgrading to the latest 10.8.2 (including the graphics update) and resuming from overnight sleep, all Apple applications (Safari, Finder, etc) are missing all icons from toolbar and menubar (see a screenshot).
This is second time I encounter the problem. At first time I did a clean reinstall of Mountain Lion (i.e. wiped the disk) and did not install the latest OS X updates. When I yesterday updated OS X (after a week), today the problem was back after resuming the machine from overnight sleep.
rm -rf'ing all files under /Library/Caches and ~/Library/Caches and rebooting did not help for me. I filed a bug report at https://bugreport.apple.com.
After reading this thread, I re-booted into safe-mode, then back to normal mode and the icons are now back. I disabled hibernation as a precaution, until Apple will fix the problem.