"Cookie Cutter" is a way of referring to a Deck that is created mostly from "Splashable" cards, with little or no general theme. Often, these Decks include powerful effects, monsters with high ATK and a few with high DEF, but aren't specifically themed in any way. This term is usually used in a negative context, and as such these decks are believed to generally be used by players who only want a quick, effortless win, and believe they can achieve such a win by copying (like a cookie cutter which creates duplicates of a certain cookie shape) certain tournament-winning Decks. A similar term is netdecking.
Yu-Gi-Oh! GX - Episode 018 and Yu-Gi-Oh! GX - Episode 019 took a jab at this phenomenon with Dimitri, a character who imitated the Decks of other Duelists to the point that he imitated the Duelists themselves as a result.