What is this Hole?

It is the drain from the drink holder above. It could be coffee like Bob said or could be rust from metal or s/s stuff stored in the cup holder for a long time.
 
i assume the way way to clean it would be to flush something from the cupholder, but what product would you suggest?
 
I would flush it with Simple Green and let it soak. You might even plug the bottom and fill it with the cleaner. If that doesn't clean it sufficiently I would pour a bleach mixture in a let it work. Make sure you rinse it well if you use the bleach.
 
If that was mine, I would pull the speaker, 4 screws, and replace the $.79 tubing. Use ON/Off to clean the stain if needed.
 
Rorkin has it right... its just a clear plastic tube. Probably an bottle cap left in the cup holder rusted away and the crud will be stuck in the tube forever...