Talking to a Yamaha tech about the squeak in my 250 SHO and was told it is due to a dry bushings on the driveshaft. He stated it could be fixed with the Yamaha waterproof grease.
I decided to try the fix myself. Pulled the lower unit and directly under the splines at the top of the driveshaft is an area of about 1 inch that is supported by a bushing in the motor housing. Mine was dry and dirty. I cleaned the area with steel wool and applied the bushings area with the Yamaha grease and reassembled.
My SHO would always squeak at idle after long or hard runs. After greasing the bushings area and running for a month now....NO MORE SQUEAKING!
Hope this helps some of you guys with the dreaded squeak, an easy fix.