Polysulfide
Polysulfide (eg. LifeCaulk) is my choice for bedding everything you listed. Use acetone to clean up any mess-ups. For some reason, polyurethane (eg. 3M 5200) is a boater favorite, although every expert I've heard from says DON'T use it on anything you might ever want to remove again. Polyurethane is a powerful adhesive as well as a sealant and it's a major PITA to break the bond. Marine silicone should be used to seal windows and for nothing else.Just my $0.02. Good luck!