[aflanigan]

It depends on what type of material your ports are made of, and what mounting desing (flanged or clamped).

See this article by David Pascoe on rebedding portlights:

http://www.yachtsurvey.com/WindowRepair.htm

"To reset the glass, use a silicone based window glazing SPECIFICALLY designed for this purpose. Do not use plain old silicone sealer."