Maximum of 3 Rule

Between your Main Deck, Extra Deck and Side Deck, you may only have 3 copies of 1 card of the same name. Here are some examples:

Example 1
You may not have more than three monsters with the same name printed on the card. For the example of Harpie Lady 1, Harpie Lady 2, and Harpie Lady 3, its effect only activates when it is designated by a card effect specifically asking for Harpie Lady, at which point a player may select Harpie Lady 1, Harpie Lady 2 or Harpie Lady 3 as a target of that effect. The fundamental rule that this follows is that monsters in the deck and graveyard don't get their effects unless they are targeted by a card in play. To say otherwise means that all cards in the player's deck have overlapping search/targeting effects that can activate with any target.

"Harpie Queen", on the other hand, only has it's name treated as "Harpie Lady" while it is face-up on the field, or in the Graveyard, but not in the Main Deck, so you can have 3 copies of this card, in addition to any legal combination of the above cards.

Example 2

 * Proto-Cyber Dragon only has it's name treated as "Cyber Dragon" while it is face-up on the field. It is not illegal to have 4 or 5 cards on the field that all have the same card name, if the name change is only applicable while on the field and not in the Main Deck. So, you may theoretically have have 3 copies of "Cyber Dragon", and 3 copies of "Proto-Cyber Dragon" in your Main Deck. However, Cyber Dragon is limited for its power, reducing the amount you may have in a deck.

Example 3

 * Cards that are similar in name. For example:
 * "Battle Ox" and "Enraged Battle Ox" have different card names.
 * "Obnoxious Celtic Guard" and "Celtic Guardian" have different card names.
 * "Swift Gaia the Fierce Knight" and "Gaia the Fierce Knight" have different card names.
 * "Black Luster Soldier" and "Black Luster Soldier - Envoy of the Beginning" have different card names.

In the above cases, a duelist may theoretically have up to 3 of each card above in their Deck. These cards are seen as Retrained from the original Normal Monster or Ritual Monster version of the card

Example 4

 * Cards that are stored in the Extra Deck and have the same name as a card that exists in either the Main Deck or Side Deck:
 * Neo-Spacian Marine Dolphin is stored in the Extra Deck, but by its effect its name is treated the same as "Neo-Spacian Aqua Dolphin" and therefore you cannot have more than three of a combination of these cards, despite them being stored in separate Decks.
 * Neo-Spacian Twinkle Moss follows the same rule.