Speed and latency is the main factor to determine how fast is your memory.
DDR3 1600 CL 6 vs DDR3 2000 CL 9.
To put it on simple maths:
The frequency is expressed in Hertz, which means "cycles per second". So, the DDR3 2000 will perform 2000 cycles a second while the DDR3 1600 will do, well, 1600.
The CAS latency is given in cycles. So, a CAS9 RAM will take 9 cycles to respond and the CAS6, 6 cycles.
Now putting it together: the DDR3 2000 CAS9 will take 9/2000 seconds, which is equal to 0,0045 seconds, to respond while the DDR3 1600 CAS 6 will take 6/1600, which is equal to 0,0038 seconds, to respond. Thus, the 1600 one is faster.