I purchased a 2006 CPO a few weeks ago and found the squeek to be quite strange. Not even my 98 Civic squeeks that much. I took it to 2 different dealerships in the area to resolve, but none could properly fix.
They claimed to have cleaned some adhesive on the seal, but the squeak would come back after a rainy day or after a few days of leaving the dealer.
It was only until the 3rd visit (yes 3X) I took it back that they replaced the door seals on the drivers side -- thankfully this did fix the issue. However my right side was acting up... With frustration at an all-time high, I read this thread and tried what 328idogg recommended (terrific screenshots), and yes he was right.
Turtle Hard Wax liquid and Vinylex works like a charm. Vinylex I found @ PepBoys, and the process takes less than 10 minutes to do.