What does the clock frequency of my miner mean. I can change it but how does it affect performance? For BFGMiner when I start my Gridseed I can press 'C' to change it.
I believe that is just a parameter to allow you to control the clock frequency (usually measured in MHz) of your miner. You can see a sample list of configurations for CGMiner here.
There is an inherent trade-off here. A higher frequency means a higher hash-rate but more energy consumption and wear-and-tear on your hardware. For example, this site shows a sample chart of different frequencies and hash rates for a particular piece of hardware. It's up to individual miners to figure out what the right trade-off between performance and energy consumption is for them.