If you're looking for a -1/-1 counter you can get one on Shapeways here.
Everything we’ve tried to use for +1/+1 counters gets scattered during a Magic: The Gathering game. Usually it’s little squares of paper ripped off our scorekeeping sheet, but then they fly hither and yon when someone taps a creature.
So I made these counter clips. Plus one clips slide onto the left side of the card, minus one clips on the right. The clips interlock so an X/X boost makes a neat line of counters on the card’s edge.
Important question: Will this damage my cards?
Probably not. I wouldn’t put one of these on your near-mint Black Lotus, but the amount of wear and tear it puts on your $0.05 goblin card is probably less than you’d get from an anemic shuffle. Friction holds these clips to a card, but they’re very easy to remove.
You should have that Black Lotus in a helium-filled, hermetically-sealed Lexan box anyway. Hidden. Dark and deep in the vaults, not to be used, unless at the uttermost end of need.
You can download this model and others like it for free at The Forge.