Well, this is an opinion question so I will give my opinion.
Threebond (same as yamabond, kawibond, etc- I really believe all the same thing with a different name) is my choice for places that are a little shaky as far as good mating surfaces. This is a semi drying compound, so any that squeezes out into the motor itself will break up and not plug up the pump or oilways. Thats not to say you should not be very careful and use it sparingly.
Silicone of any kind is a no-no in my book. It dries very stuff, will break off, and is not going to break up in a motor. Those little balls and worms of silicone will plug things up. Plus, when I go to any kind of show and see things put together with orange or blue silicone sticking out at every mating surface I automatically think "guy had no idea what he was doing, wonder if the rest is put together that badly". Prejudice? Maybe, but it is an opinion thread.
For paper gaskets I like Gaskacinch. Spread it on both contact surfaces, both sides of gasket, gently place the gasket and done. This stuff has been around forever for good reason. I imagine they will still be making it 50 years from now also.
I wonder if anyone will start making gaskets for us out of the new composite materials Harley and the others use. I cannot recall the name of them right now, but no sealant necessary and they are good over and over (or so they say, but then again most of those guys dont mind if they are lubricating the driveway every time they park
)