I have the same issue on my passenger side front door. Makes almost a creak sound.

I recently investigated and found that one of the plastic fingers on the panel that slide down and interlock to the door shell had never been properly installed....this was evidenced by the fact that the white plastic liner was never broken at that point. However even after correcting this, it still makes a creak sound, only not as bad. Need to look at again in more detail.

As to the door sills...I lube mine with 303 Aerospace protectant. Works good, but wears off quickly.