Over the years I have read lots of instructions on how to properly clean an essential oil diffuser. All of them a little different, but all adamant that you be very careful not to damage the metal disk at the bottom which is responsible for aerosolizing the water (and oils).  Through lots of trial and error I have determined this to be the best method for me:

Items needed for cleaning

Dirty brown residue on diffuser

1. Fill the water reservoir half full, and add in 1/2 teaspoon white vinegar. I probably use more vinegar than this since I don’t measure and just pour some in, but let’s stick with 1/2 teaspoon to be safe. We don’t want to damage anything. Run the diffuser for 5-10 minutes to allow the vinegar/water mixture to work through and loosen up the gunk. 
2. Turn off the diffuser, unplug it, and dump the water out. Be extra careful when you dump, as getting any water into the underside of the machine or into the motor area will ruin it.
3. Then wipe out the inside of the diffuser with a soft cloth or q-tip.  Don’t use anything like a brush or toothpick that could scratch the ultrasonic disk in the bottom.  Pay special attention to cleaning the metal disk as these often cause the most issues when they get dirty (a q-tip  works especially well here).  You can use a drop of lemon essential oil on your brush or q-tip if you need to cut through extra grime.
   

   Don’t forget the crevices in the top.

   

   
4. Also pay close attention to the hole and crevices in the top of your diffuser as they can get clogged with build-up as well. Again, a q-tip works well here.
5. Cut a “magic eraser” into 1″ squares, wet them, and use to remove stubborn stains on the plastic (inside and out). Just remember to avoid the silver disk. This will make your diffuser look almost like new!
6. Wipe all surfaces with a soft, damp cloth to remove any “eraser” residue and it’s ready to use.