Well... the CPU fan is for the fan on the CPU, while the chassis fan is for fans on the case (aka chassis).
All right, enough with being a smartass.
The CPU fan has a speed regulator which is controlled by the temperature profile in BIOS based on the temperature of the CPU. CPU gets hot, the fan speeds up to compensate. CPU cools down and the fan slows down, and in some cases can turn off entirely. These are typically 4 pin fans, but are compatable with 3 pin fans (for example I have 2 3pin fans on my CPU cooler as my motherboard has 2 4pin CPU headers)
Chassis fans are typically 'dumb' fans which spin at a specific speed. If you want your fan to spin slower/quieter then you add a fan line resistor. If you need more airflow then you buy faster rated (and typically noisier) fans, or you can put more fans in the system.
Mid-level motherboards will have a little bit of logic onboard so that you can set your case fans to an arbitrary speed, or set them to a predetermined 'low, medium, or high' setting within BIOS to select your best compromise between noise and airflow.
High end motherboards have a full fan controller onboard. This lets you link your fan speed to a temperature sensor, allowing you to speed up all of your fans if your case, CPU, or GPU reach a specified temperature. This is very nice as it allows you to never have to think about your case temperatures when OCing or gaming, where on a cheaper motherboard you would have to manually set your fans to high beforehand.
Another neat tool is speedfan. This is a software based fan controller which works with most motherboards and allows you to set your individual fan speeds from within Windows. The issues of course is that it is at the software level, not hardware, which means that if the software environment crashes, then it does not control your fan speeds properly which can potentially cause damage. Also, it is a really old program, and has 0 support, so if you run into any bugs or issues then you are SOL.
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