A squeak needs sliding, and the seal is the only thing that slides
Three things on a door can make noise, and they make different noises because they are doing different things. The seal is rubber pressed against painted steel. The door check is an arm with a friction pad inside, holding the door at an angle. The hinges carry the weight — fifteen to thirty-five kilograms — on two pins. A squeak is high-pitched and continuous; a clunk is a single thump; a click happens once, at one angle.
That gives a test that takes one second and no tools. While the door is squeaking, press one finger hard on the seal and hold it there. If the squeak stops dead, you have found it: you have stopped the relative movement. And the mechanism explains why it sounds like that — rubber on paint does not slide smoothly, it sticks, loads up, lets go, sticks again, tens of times a second. That is stick-slip, and it is why the noise stops in the rain (a water film lubricates it) and gets worse in the cold (rubber hardens and grips harder).
And it is why the standard advice is wrong. Oil on the hinges cannot fix a noise coming from the seal, because the hinge is not moving when the door is shut and the car is going over a bump. Worse, the same instinct applied to the door check destroys it: the check holds the door open by friction, so oiling it makes the door swing shut on its own — on a slope, onto a hand.
Three faults, three tests
Squeaks over every small bump, stops in the rain is the seal. Clean the rubber and the paint it touches with a damp cloth and let it dry — grit in the contact patch is half the problem — then apply silicone grease or plain talcum powder thinly along the seal. Silicone, not mineral oil: mineral oil swells the rubber and then ages it faster, exactly as it does to a fridge gasket.
One click at one particular angle is the door check's friction pad, which is a wear item. Confirm it by holding the door at that angle and rocking it a few centimetres: the click should repeat in both directions. A check is a bolt-on part on most cars and an inexpensive one; replacing it is the fix, and lubricating it is not.
A clunk over bumps, or a door that needs a slam is the hinges: the pins wear, the door drops a couple of millimetres, and the latch then meets its striker too low. Test it by lifting the door by the open edge with the door half open — any vertical movement is worn pins. Adjust or replace the hinges; do not solve it by slamming, which wears the striker and the latch.