When laying or marking out a project, depending on the task at hand I've been known to use a carpenters pencil, a mechanical pencil, a blue pen, a piece of chalk, and a marking knife. As I had the camera in the shop for a few progress pics of the shaker table I took a couple of photos to show how I attempt to accurately mark out cuts.
Step 1: The Marking Knife
The marking knife is the most accurate as it leaves the thinnest line. It also has the advantage that you can place a chisel easily and accurately in the resulting groove. It's disadvantage is you need to be aware that areas you cut will show in the final piece. The most important thing when selecting a marking knife is that it is diamond shaped so you can mark left and right sided. Here I'm using a Vesper Tools marking knife.
Step 2: The Mechanical PencilA 0.5mm mechanical pencil will follow nicely along the groove made by the marking knife. This highlights the otherwise dull groove.
Step 3: The Eraser
This tip I picked up in one of the woodworking mags. By quickly running an eraser over the line you remove all the pencil other than that in bottom of the groove.
Step 4: The Chisel
The final step before reaching for a saw involves the chisel. Deepen the groove vertically (being careful not to bruise the fibers on the project side.) Then from waste side pare back to your line about 2-3mm, creating a |/ groove. This creates a track for your saw or chisel to work in.
The End Result
One of the end cap tenons for the table.