use 3M's 5200 semi-structural marine sealant or the quicker-drying 4200 version. Both available in black, white, brown and clear - as far as I know those are the only choices, but I could be mistaken. I've probably used gallons of the stuff by now (well, quarts at least!
) doing exactly what it sounds like you need to - completely rebedding all of my cockpit hatches and windows.
cheers,
Blue Eagle