I drill out the holes slightly bigger than current to remove any sealant or heaven forbid silicone someone might have added and expose good clean wood/glass. Then I use epoxy with thickener added... if you don't want to mix epoxy get some marinetex
Whatever you use, a toothpick works well to work it in to the back of the hole.
http://www.google.com/aclk?sa=l&ai=C...rd%3Dmarinetex