Good Afternoon.
In the cgminer archive there is a file called SCRYPT-README.txt. It does a fairly good job of explaining the performance tuning process for Scrypt mining.
Off the top of my head the biggest performance gains for me were tuning the thread concurrency. I couldn't get the auto-fan and auto-gpu options to "stick", so I coded them as command-line options into my startup script. This was important for me as my card throttles noticeably at higher temperatures. (on Windows)
...It's 30 degrees today and the miners are keeping my bonus room toasty warm.

FarmerGreene
ExtraParts.info