I am just putting this up as an FYI, and your mileage may vary, but I had a bluetooth keyboard connected using a d-link dbt-120 and was getting cracking and stuttering sound in most emulators. This was happening using both hdmi and analog sound, overclocked or not, and at any screen resolution.
On a fresh Raspbian install, without the bluetooth drivers/software, the sound was much, much better.