I did this on Craftsman wrenches and socket sets of various vintages ranging from my father and grandfather's to current. Most had deep engravings of the tool sizes. It was more difficult to get it to work with very fine markings found on some of their smaller 1/4" drive socket wrenches. Some of the finer markings required more than one attempt. I'm not sure how well this works on laser etched tools that became available in more recent years. I would think that quickly wiping off the paint with a dry towel will work, but the effect would be more subtle. The good thing is that I could completely clean off the paint with lacquer thinner if the results were not to my liking.

Materials

Hand tools to mark
Oil based paint marker, avoid extra fine tip if possible. Sharpie oil markers work well. Optional: Contrasting colors to suit your categorization needs.
Shop towels or rag
Lacquer thinner

Reasons to do this

Make it easier to spot the right tool size quickly.
Using contrasting colors make metric and US/SAE tool sizes easier to differentiate in a pile of tools while I am in the middle of a job, particularly if I'm not returning them to their storage locations right away.
Looks nice and is customized to you
Cheaper than buying a certain name brand that offers enameled lettering

Step 1: Prep Work

Clean off heavy dirt and oil deposits from the tools with a towel and some lacquer thinner, acetone or other solvent that evaporates quickly. They don't need to be clean enough to eat off of, just clean enough to allow paint to adhere well.

Step 2: Apply Paint

Scribble over the size markings with the paint marker. You want to lay on the paint fairly thick. I started with one tool to see how the color turned out, then worked in batches of 20-30 tools.

Allow the paint to dry for a hour or two.
Note: I used two contrasting colors to differentiate between metric and US/SAE tool sizes. You could also use one color for the lettering and another for the size. It's really up to you on how to customize your tools.

Step 3: Removing Excess Paint

Apply a small amount of lacquer thinner to a shop towel. I had a spot about 1 - 1.5 inches in diameter. Lacquer thinner flashes off rather quickly so soaking the towel will just be wasteful and make excessive fumes.

Gently dab the dried paint once or twice to soften the surface. I found rolling the tool through the moistened towel works the best. Ideally only the surface paint is softened up while the material down in the crevices remains relatively dry. You should still have seemingly heavy deposits of paint on the tool surface, this is okay if you work quickly.
Note: You could just wipe the paint with the lacquer thinner, but it seemed to strip too much out of the crevices. If this happens just mark over the surface with the paint marker, allow it to dry and make another attempt.

Wipe the excess surface paint off of the the tool with a solvent free part of the shop towel. Most if not all of the surface paint should come off with a few seconds of rubbing. A hard object finger nail or small piece of wood like a Popsicle stick backing up the towel can help. Note how there is a bit of paint remaining on the surface in the picture. It should come off easily if you work quickly while the paint is still softened.