I usually write on the side than tape scotch-tape over it. And I double-label the tubes, with numbers on the lid (with a chart on the side what does each number mean).

There are waterproof or organic solvent proof pens commercially available. Furthermore, you could by laser printer compatible labels (available in different sizes),  that suite your need (I use them to label tunes for cryoconservation). The ones I use are made for a range from -196 to +140 degrees Celsius. Hope this helps

I took waterproof/organic solvent proof pens as a standard labeling equipment. Anything else is not reliable. 

You are right, I do not rely on the labels solely. Usually I just combine the different methods, I used to have solvent proof pens and the smeared when I heated the tube on a shaker...  so you probably want to make sure to label each tube at least twice to be sure

www.labtag.com has some pretty good, diverse products that resist water as well as organic solvent, you'd probably find something there