Use a FIFO :)

(This solution may not scale well if there are many directories, but you'll be able to adapt to your case)

Create a fifo (mknod -p fifoname) and have a script continuosly read from it. If there's nothing in the FIFO the process won't consume resources.

Programs to run are simply inserted in the FIFO as strings; in the cron job, you substitute the script execution with a write into the FIFO, i.e. you prepend echo and append a redirection to the FIFO. The reader script will extract and execute them, via some eval mechanism, or fork(), or whatever you like.

There are tons of theme variations, but I think this should give you the idea.

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