Apple - runaway distnoted process
I've seen this too. Emacs 24.3.1, Mavericks 10.9.
I've found that the distnoted process calms down within seconds after I quit out of Emacs.
I've filed an Emacs bug here: http://permalink.gmane.org/gmane.emacs.bugs/80836
Summary from the OP: This was a great tool for debugging. It originally pointed me to Spotlight reindexing the filesystem, but I narrowed down the things it's allowed to index, and I still saw the problem. I ended up setting up a cron job to kill distnoted regularly. See answer farther down.
You can debug distnoted by creating the file /var/log/do_dnserver_log
This causes the CFNotificationCenter server (distnoted) to record information about all notifications to the system log.
I would start there, reboot and look at the system log when the CPU spikes up. This should out the culprit easily.
More info on CFNotificationCenter debugging can be found in official Developer docs here: Technical Note TN2124 > CFNotificationCenter
I know I'm late to the party but this is a memory leak specific to Cocoa emacs on Mavericks that is fixed in the trunk. For now there is a patch you can use to build emacs 24.3 with just the fix.
https://gist.github.com/anonymous/8553178