I am designing a simple synth with Arduino (just the Atmega IC) and it 
works fine. The only thing is this annoying clicks I barely hear 
constantly if I raise the volume somewhat.

I had this problem in the past that's why I was trying to fix it by 
designing the PCB, separating 3 ground sectors in digital and analogue 
parts on one side of the PCB. In theory that should stop the digital 
part contaminating the analogue part. It seems it didn't quite worked 
because I can still hear the clicks.

There are two things making clicks at the same time, according to my 
tests:

  [1] the Atmega crystal: If I remove the Atmega IC, that click stop. 
**UPDATE: **That click was caused by the Atmega program. But I still 
have this other midi click sounds:

  [2] the Midi messages: When Midi is not connected, there is no click. 
After each midi message is sent (a note or clock i.e) I hear a click. 
For example the clock makes a constant stream of clicks and are sped up 
if I increase the tempo on the master device sending the BPM. If I take 
the Atmega IC and send midi messages, I can hear the clicks, so it's 
independent of it. That's why I'm thinking it's a PCB design issue

To strip down the problem I removed the LM358( 
http://www.kynix.com/Detail/1319286/LM358.html ) part where the 
"scissors" are in the schematic picture and I just get the output from 
where it says PWM, that's just the output from the atmega IC.

So, my question is: Do you see any PCB design flaws? What could be 
causing the click noises?

Thanks!!