I definitely like insulated cable staples for running Romex inside walls and ceilings.
For train layouts, I prefer Cable Clamps like these. Attached with screws, it's easier to remove or add wires as circumstances may change in the future. Often I will only run the screw through the back hole as I'm still running wire to make placement (and removal) easier.
For a layout already having scenery and buildings, not jarring everything by hammering in staples is also a plus.
I'm with Steve. I use these all the time. They are very versatile and wire pulls through them easily. Other than a Arrow T-25 staple gun to hold wires right where they come through the surface, I don't staple any wires under the layout.