Small items (e.g. glass beads) may be used as markers and placed on top of a player’s own library or graveyard as a reminder for in-game effects. These markers may not disguise the number of cards remaining in that zone nor completely obscure any card.
Players will often put something on top of their deck in order to remind them of an upkeep trigger, such as rebound, and occasionally players will put something on top of their graveyard in order to remind them of some continuous effect. “Small” is very subjective, and there are stories of a player using a plastic fishbowl to completely cover their own deck to prevent them from drawing a card before remembering the upkeep trigger. The key rules are that the item can’t obscure the cards, can’t make it difficult to see any revealed cards, and can’t be a card itself.
Players using markers to represent in-game components (e.g. permanents) must have a way of clearly representing any in-game status, such as whether a permanent is tapped.
Players will often use dice, beads, coins, or other such items to represent tokens. This is perfectly fine, but they have to be able to show whether or not they are tapped.
Sleeves or card backs that appear similar to any player’s sleeves or card backs may not be used as markers.
We try to keep the game state from getting unnecessarily confusing, so having something represent a token and not making it obvious that it’s a token is a bit of a problem. Since sleeves and card backs can be mistaken for actual cards or for morph creatures, they’re not allowed if such a confusion could arise.
A tournament official may disallow the use of game markers that can cause confusion or that are deemed inappropriate or offensive.
We’re always aiming to create a welcoming environment at Magic events, and just like with behavior, alters, and shirts, sometimes a player’s custom tokens can cross the line. If a judge believe something a player is using caused some disruption or discomfort, the judge could also accompany this with an Unsporting Conduct — Minor penalty. Additionally, if it’s unclear what exactly a token represents, a judge may request they use some other method to make it more clear. There’s no clear-cut line here, so the use of judgement from Tournament Officials is needed.