Like Tracy said, I toss the end seals, but I like Permatex #2 around the water passages only, on both sides of the gasket. But also like Tracy said, some gaskets with the printed type seal don't necessarily benefit from sealer. I don't like using those, because I think using sealer works better, since I can regulate how much sealer I use.
Oh and don't forget. Put sealer ON THE INTAKE BOLT THREADS TOO. If you do not, oil will migrate up the bolts and pool on the intake and leave you wonderin where the hell it's comin from.