Scribe or Razor Blade
The measurement and layout lines must be marked precisely. A pencil is too dull. The timbers may be large, bulky, and unevenly hewed… but the joints must be measured/marked perfectly if they are to fit perfectly. A single-beveled or double-beveled blade of some sort works better than a pencil.
You can use a standard utility knife. Make sure to change the razor blade at the first sign of it becoming dull. A dull blade will wonder and make you press harder to achieve the mark. Use multiple passes with the razor blade. On the first pass, press lightly, focusing on keeping the blade against the fence. Don’t let the grain of the wood throw the blade off course. Now is a good time to do some quality assurance and double check your layout. If you’re satisfied, make another 2 or 3 passes along the same line, making the scored line deeper and deeper.
Some people prefer a single-beveled blade. A single-beveled blade is like a chisel, flat on one side and beveled on the other. The flat side can ride along the framing square, whereas the edge of a double-beveled blade will be astray of the line by half the blade’s width.
Some text about marking tools. How to make a marking knife out of used spade bits. Where to get C.Swartz style marking knifes from Enco, timber scribes, marking/mortising gauge
A marking guage is a block of wood that slides along the timber marking as it goes.
A typical marking guage for general carpentry is too small. A panel guage for cabinetry can be used for timber framing. You want a marking guage with long, deep fence; it’ll ride along the corner of your imperfect timber and still scribe a straight line.
You don’t need a race knife or a hook knife. You can just as easily use a pencil, crayon, or chisel to label the timber. Marking the timber allows you to find it later when you’re assembling the frame. You don’t have to mark all the timbers, just the ones that are interchangeable. A lot of your common timbers (rafters, joists, purlins) will be interchangable and won’t need marking.
A race knife is a small u-shaped gouge that can carve shallow trenches in the timber. A lot of old timers used roman numerals to identify timbers because a chisel is straight and so are roman numerals. A race knife allows you to cut curves, and it’s a lot faster than using a chisel.
Nowadays most people who build a timber frame want to see the frame from the inside. Carved marking in the wood may or may not be desired. In the past the house would most likely be plastered, covering any marking from view.