This issue was driving me crazy, but I was too lazy to go and find the patch… This article makes it extremely easy; I have just built and installed Emacs, will see in a couple of days it it solves the issue.
With Emacs 24.3 (and possibly earlier versions) under OS X 10.9 there is a nasty problem that causes distnoted, the OS X distributed notifications daemon, to periodically suck up processor resources and basically tie up the machine. Sometimes it recovers on its own, sometimes you have to restart Emacs. That is particularly apt to happen after waking up from sleep mode.
The problem is fixed in the 24.4 release and I’ve been ignoring it while I waited for the new release. The other day, though, I ran out of patience and hunted up a patch I’d seen for it some time ago. If you build Emacs from source, it’s trivial to apply it: just follow the instructions in the patch commentary.