I'm considering replacing the stock speakers in my 2002 TJ Exec. I'm only after a cheap upgrade, e.g. $60 fronts, $90 rears. So basically just swapping out whatever the stock speakers are with some branded 50w fronts and rears. Is it even worth doing though? How good are the stock speakers in the TJ?

Definitely worth doing. You will get cheaper ones than the prices you mentioned and they will still be way better

Cool. Just ordered a set of 3-way 6" fronts and 3-way 6x9 rears, both Kenwoods, for $129 :D