Pros for BJT:

BJT's at the same physical dimensions and price can usually give you a lot highe
r speed, as they have very little input capacitance.
BJT's can give you a lot higher gain. Just take a bunch of components and compa
re them, and you'll find the BJT's give you better gain characteristics and ther
efore require fewer gain stages.
BJT amplifier stages are much more linear than MOSFET amplifier stages, as the g
ain doesn't depend on the bias voltage. This gives better fidelity.
BJT's are capable of handling higher output currents for signal outputs and can
have lower output impedance. In amplifiers intended to drive a low input impeda
nce load or deliver significant amounts of power, this is a huge advantage. Man
y of the highest quality op amps are made with a BiCMOS process using a BJT pair
for the output buffer stage.
Cons for BJT:
BJT's are current-operated devices rather than voltage-operated. Most of the ti
me this means higher power consumption.
BJT's have an input-output relationship that can be basically inverted by biasin
g the terminals opposite to their intended design. What this means is that a sl
oppy amplifier design can much more easily end up with positive feedback and the
refore go unstable. I've seen this before in one of my earlier designs in schoo
l, and the TA didn't figure it out. (I did, but not until much later).
BJT's have lower input impedance. This means a higher output impedance device m
ay not couple very well to the input of a BJT amplifier.
BJT's are harder to scale. FETs are easy.
Related: BJT's have pretty significant variations from transistor to transistor
, while FETs don't as much.
It's harder to make a good current mirror out of a BJT than a FET.
Pros for MOSFET:
They're really easy to scale. Want precisely half the current? Just make the g
ate half as wide.
High input impedance. At low frequencies, essentially infinite.
Since the outputs are controlled by input voltage instead of input current, they
consume can consume very little power. The reason CMOS logic won out over othe
r process technologies is power consumption, combined with scalability. In a CM
OS circuit, gate to gate power is only consumed when the circuit switches states
, while other logic forms consume power to stay in an "on" or "off" position.
Considering that most digital circuits are CMOS, using FETS for analog circuit d
esign is much, much cheaper than using BJT's because it doesn't require a whole
extra set of process steps.
It's pretty easy to make MOSFETs nearly identical. Transistor-to-transistor mat
ching is simple.
MOSFETs are easier to design stable circuits with. Unless you add feedback, the
y don't all of a sudden act upside-down and go unstable.

Cons for MOSFET:

Not as high of fidelity as BJT, since the gain will vary slightly as you increas
e the input voltage (that is, it will generate some very weak harmonics).
Input capacitance. The higher the gain, the greater the input capacitance thank
s to the Miller effect.
Can't drive a low-impedance load very well.
Low gain per part, which often means more amplification stages are necessary for
higher gain, even when using advanced design techniques. Each amplification st
age adds noise -- that is, you can never, ever get a better signal-to-noise rati
o at the output than at the input.
This list is not comprehensive. It's just the best I could do off the top of my
head.