I used to fill my books with so many little bookmarks they spines had trouble coping. I often doodled as I read, and the doodles ended up on the bookmarks, and I could find stuff by looking for the doodle I'd marked it with. A non-doodler might have a better picture marker to look for if he got a set of little stickers, picked an image per class, and stuck, for eg. the watermellons on all his math stuff, the cantaloupes on all his science stuff, etc. (Or on a post-it that sticks up a little from the top of the page, and can be removed before handing in... more visible, AND reuseability, so there.) Plain coloued dot stickers might be enough, and seem more masculine.
(Oh sheesh, I'm discussing gender steriotypes and following up on JonLaw. Are we about to talk about coffeepots again? (sorry, that was another thread))
Stickers are my solution to everything.
Luckily, my older son agrees with me.