Might be a bit pendantic with the terms, but caulking is as much of a technique as it is a product. When I think of caulking I think of process by which a seam is filled with a substance in the hope of stopping a leak.
Used in this capacity, there are precious few examples where caulking a joint is a good idea on a boat. If you want something to seal, you simply can't squirt something into a joint and hope it seals on its own accord.
Instead, you need to "bed" components if you want to seal them and that means capturing a sealant between two surfaces and using a mechanical form of fastening to keep the sealant in place. For this kind of bedding, I like 3M101 and Lifecaulk (Boatlife is the brand not a product). I'm just comfortable and confident in the lifespan of polysulphide based products used as a bedding. I would not turn down something like 3M 4200, the polyeurethane's are fairly well proven at this point where they are formulated primarily as a sealant.
You want to stay away from the more tenacious polyeurethane products like 5200 unless you absolutely need the nasty adhesive properties. In a bedding situation you already have a mechanical means of securing the joint and so neithe need nor want the adhesive.
