Polysulfide, polyurathane(5200) and silicone all have their proper places.
Polysulfide should be used when the item being bedded will have to be removed some time in the not to distant future. It''s sealing and adhesive properties are very good(it also can take gelcoat with it when removing a bedded item)but not extremely long lasting and should not be used for things like cap rails, cleats hull-to-deck joints etc.
I''m quite fond of polysulfide,about the only thing(besides the smell) that I don''t like is that it cannot be cleaned-up with denatured alcohol.It has to be cleaned-up with serious solvants like laquer thinner or mineral spirits and because of this it is harder to clean.
5200 is my personal favorite.It''s bonding and sealing properties are excellant will last decades and is cleaned-up easily with denatured alcohol.Do not use isopropal alcohol because it has water in it and tends to smear and not remove.
5200 and polysulfied bedded items CAN be removed. This works for me: After applying , tighten down to 1/8 of an inch, clean the edges with denatured alcohol, let the compound cure completely, then tighten down the rest of the way. This means you have to apply it thicker so that later(much later)you can use a long bladed flexible knife to cut the bedded item free. Some people use a hacksaw blade. A bread knife is what I use.There is a new product on the market that claims to break down polysulfide and polyurathane, but I''ve yet to use it.
Silicone is a poor adesive but a pretty fair sealant does not last a very long time and is unsuitable for 90%-95% of all aplications. I never use this stuff except for plastic ports.Polysulfide and polyurathane will attack the plastic.
If you use silicone with fixed portlights, like the ones on Bayliner power boats,it has to be applied to the base surface in a bead then the window put in place and the screws tightened until you start to see the bead spreading out. Then, since it cures so quickly, finish tightening in a half hour.
With the other two sealants in mention you can be more "careless" in the application but silicone is a poor adhisive so for lasting power it is a little trickier to apply.