Most of today's ICs use MOS technology cause they're easier to implement (so they can be reduced to smaller sizes than BJTs) and consume less power (when used as switches). These advantages are very important when you have to design digital circuits, and since digital circuits have overtaken the market nowadays MOS technology is prefered over BJTs. Nontheless, there are a couple of aplications that use BJTs (since they are faster than MOSFETs), like RF circuits. BJTs, used as amplifiers, can generate much higher gain than MOSFETs, and that's why there are also technologies that use both MOSFETs and BJTs (BiCMOS) to take advantage of both kind of transistors.
diemilio