The original '72 Fireball.
Banzai Run has a devil of a skill shot.
Old Bally games that require a bounce on the arch to activate the big points.
Cyclone is righteous with the plunger.
Pinball Magic Loop/drop skill shot is always fun.
The AFM/MM hold the left flipper and make the shot at speed are very well implemented with a nice touch of risk/reward.
I also like games like Lotr that give you different options that you have to execute with.

There's more than that, but I'm keepin this one short.

In summary... the shot that requires you to execute it "skillfully".

and if you are really skillful, the mini-orbit on the other side of the PF for a cool 10 million! 13 million points is a great way to start a ball on PotC!

Medusa has a fantastic skill shot as well.

Worst skill shot has to be TZ. Make the skill shot, lose the ball out of the pops.