How to choose a bypass capacitor for a common emitter amplifier?
It depends on the bandwidth you want the amplifier to achieve. A simple thumb rule is that a capacitor is seen as a "short-circuit" at higher frequencies and an "open-circuit" at DC. 

Therefore, the gain of a common-emitter is about the load connected to the collector divided by the load connected to the emitter. So, you can change the AC gain of the amplifier using a capacitor at the emitter in parallel without changing the bias point of the transistor. A .1 uF in parallel with a 1k resistor will put a low cut frequency of about 1.6 kHz. Therefore, higher values should be used for lower frequencies.