Where did the value of 0.1uF for bypass capacitors come from?
Higher value capacitors will not be as effective at dealing with high frequency current drawn by the chip. Above a certain frequency a capacitor will start to behave like an inductor. The value where its characteristic changes is the series self resonance of the device: -



Thus, you'll find that on microwave devices 100pF capacitors are also present as decoupling along with the bulk capacitors. Here's an example of three capacitors decoupling an FPGA: -



The black curve is the composite impedance of all three capacitors used. Taken from here.


  Where did the value of 0.1uF for bypass capacitors come from?


It's a good compromise between bulk and high frequency capacitance BUT if you are designing radios your default decoupler may be 10nF or 1nF (UHF). If you are designing really high speed digital stuff you may also use 2 or 3 different values in parallel like in the FPGA picture above.