I feel as though I'm in the minority on this subject, but I have basically stopped using highlighters since starting med school. The only time I use them now (and its still only a yellow one!) is if I'm reading a textbook, which is happening less and less as time goes on. The compulsive highlighting with multiple colors that I see happening kind of drives me nuts to be honest. If you want a coloring book, go get one at Walgreens!
That being said, I do use different colored pens. During lecture, I only use one color, something other than black so that my notes stand out from the printed handout. If I wrote it down, it must be important. Then, when I go back over lectures, I use a different color and either circle or underline important concepts. Then, the third time I see the lecture, I use yet another color and either circle or underline, whichever I didn't do the first time. This system used to be a lot worse, until I couldn't remember which color I used for what and just gave up 🙂
Moral of the story I really think is this: most people in medical school are incredibly Type A and anal about everything. Therefore, we must have some "system" to feel more in control of our lives. This seems to involve, for many of us for some odd reason, very intricate systems of colored writing utensils!