I am fortunate that my machines have different colored bobbins so I can tell them apart. What I do have issues with is the thread! I have bobbin thread for embroidery, that is easy as it's 80 wt. I do need to differentiate between my quilting threads, and regular sewing threads, I think I will put a dot of nail polish for quilting threads. i have a permanent sharpie but find it rubs off eventually.

I use a Sharpie marker to mark with a dot if it is a special bobbin.

I have separate boxes that I labeled with the machine name. 2 of my 3 machines are Janome and can share bobbins so really I only have to keep 2 separate bobbin stashes.

For telling thread apart once it's wound on the bobbin, I distinguish only between cotton & poly. Cotton bobbins get those children's terrycloth mini-scrunchie things to hold the thread; poly gets a slice of clear tubing to hold the thread. (Both tips I got here!) I sew with a couple different weights of cotton thread but I can usually visually tell by comparing the bobbin's thread to a spool's thread which weight it is. At least close enough that my machine doesn't mind.

Since you said all 3 machines take similar looking metal bobbins, and it sounds like you use all three regularly (?), i would suggest nail polish dots--Blue for Bernina, Orange for the O in JanOme, and nothing for the FW .

I have different Bobbin buddies for my machines. Luckily, the Janome bobbins are plastic while my FW's are metal.

I use sectioned fishing tackle boxes which close tightly. I also keep the bobbin boxes with the machine they go to.

I also use the sectioned fishing tackle box for my LA bobbins.

i have several machines also. there are classes of bobbins, according to sewing/quilting catalogues, but i don't k ow what is what. so, my fw bobbins are kept in the little baggie they came in, my janome 1600P bobbins are kept in the toolbox that came w it, my plastic bobbins that came w my pfaff are kept in the swing out tool tray that is part of the machine deck. bobbins are precision tooled & balanced --i would not put any nail polish, marking pen ink or anything else on a bobbin. a little time to keep them organized is very simple. if in doubt, check w your local sewing machine repair person.

I have a bobbin tower by each of my machines, but I also use a sharpie to mark an initial on the top of each bobbin, so if they do get misplaced, I'll know...
http://www.connectingthreads.com/Too...9APxoCqPjw_wcB
of course..I also have a bin of bobbins that I'm not sure about..on my rainy day list! LOL

They aren't such a precision instrument that a dab of nail polish or a letter written with a sharpie would mess them up...otherwise, how could we use different weight threads? They are exact as to their height and diameter, but a little marking won't hurt anything.