In places where your circuitry touches the board, use a plastic insulating material (it can be bought in sheets, typically black). Be careful to clip away sharp bits.
Use 3mm and 2mm screws as appropriate. IIRC, the Pi boards all use 3mm, whereas PTH boards typically use 2mm.
A hard laminate is more rugged than a pure type of wood - always predrill with a 1-2mm drill, directly through the board’s holes if you don’t like rulers and pencils.
The advantage is very clearly that - in addition to wood being a great insulator - that you can use old school wire wrap to supply various voltages ad-hoc.
http://www.instructables.com/id/Use-a-real-Bread-Board-for-prototyping-your-circui/
If you use nails or screws, strip some wires, wrap the copper filament around the nails/screws, and solder it a bit to fix it in place.
If you need to route some wiring nicely, use small nails to make corner posts.
Contacts etc can be embedded in this material even more easily than in ABS plastic.
I personally use plexiglass, which is a bit brittle, and requires care when drilling. But it looks a lot less cr?pp?.
Usually I just lay out the bits and get approximate X, Y, then have a goon at the hardware store to cut it for me.