Absolutely wear a filter mask and eye protection if you're going to be sawing/grinding/sanding PCB's. If you don't have a filter mask, use an old T-shirt that you've dampened.
I've used a sheet metal shear, a large paper cutter, nibbling tool, aviation snips, jigsaw, Dremel, etc. If you're going to use a saw, use a blade with very small teeth. There should be at least two teeth in contact with the fiberglass at any one time, or else you'll get a really ragged cut.
I use a hacksaw with a fine tooth blade. I usually cut the boards outside. I always wear a dust mask and safety glasses. If I cut the boards inside I have someone vacuum
the dust as I cut.
I leave 50mils between layouts. If you go slow cutting this is sufficient space so
that you can do one cut between two boards.