- Don't write directly on the box. Put tape on both the lower portion of the bottom of the box AND the lid for labeling. You do this because lids can be separated from the box when people are digging around for something in the freezer and it's easier than looking at the tubes later when you're in a hurry.
- Use a permanent marker, not dry erase or pencil or fine-point pen. You can't see these things once there is ice on the box and sometimes things other than a good dark marker rub off easy. Also, your samples might be stored for longer than you are in the lab, make it easy on people who come after you and label things clearly.
- Include the experiment number if you have one, the type of cells or animal the tissue are from, what is actually in the box and be specific (cDNA, bacteria stocks, organs, etc), your initials (written legibly) AND A DATE.
- Make sure at least one of the labels can be seen clearly when the lid is on and the box is in the freezer insert (always point the label out when putting in storage).
- If placing in -80˚C, update the freezer map or prepare to be bitched at later when you forget where you put your stuff.
Being insanely anal in nature, I include color coded dots for boxes that go together. Anytime I see a yellow sticker (which is also placed on the tape so the boxes can be reused) I know which experiment those boxes belong to. If you only have a few colors, add a large bold letter to the center so you don't have to wipe everything down and read to spot if something is yours.
Consolidate boxes often as you process samples so you're not taking up valuable freezer space for a couple of tubes per box (update the map each time you do this!). When your awesome science has been collected and the box is empty, peal off the tape and put the "almost like new" box in a common area for other people to use. Don't horde them at your desk or leave the tape on for other people to deal with. Wouldn't you hate to do that too?
It's also a bad idea to just put a second layer of tape over the first, probability is good you're going to lose that second layer once the box has frost, so it's better safe than sorry.