The softer resins like the some urethanes and silicone will probably not be suitable for moulding, they will be too flexible. Epoxy is your best bet. I use Robnor PX700K for pretty much everything, Rapid part number 87-0220. Very easy to mould and machine afterwards, just watch the dust.
To get a decent quality moulding, you'll need to make a vacuum chamber. A 'Really useful Box' with a hole drilled in the side for a vacuum cleaner is generally sufficient unless you need the moulding to be aerospace quality. You just need to agitate and expand the air bubbles to get them to rise to the epoxy surface. If you do need aerospace quality, you'll need to degas the resin under high vacuum, but watch out if your PCB contains electrolytic capacitors or relays.
Cure the moulding overnight under a 150w halogen lamp. Before mixing the resin heat the bag to about 50C in an oven. Do not overheat! The bag should be warm enough to handle comfortably. This will make it much less viscous in the mixing and pouring process and gives a much better looking mould.
Epoxy resin will leak out of the smallest tiniest hole that even water wouldn't get through. Make sure ALL holes in the mould are sealed tight. Same with components, don't use non-waterproof relays etc.