A synergistic deck is one where every card benefits from every other card in some way or fashion. Even a deck full of seemingly bad cards can be a good deck if it showcases potent synergy. Tribal decks, such as Goblin or Elf decks, rely on synergy to win games. In contrast, decks with good cards that seem to contradict each other suffer from disynergy.
Some synergy may be connected to the decks Mana curve where the turn to drop certain cards adds to the overall synergy. It may be obvious that you must play a goblin before you play a Goblin Grenade, but sometimes cards have to be cast at a certain order. The more strict such a play order becomes the more synergy will be lost in the process. The optimal goal of synergy is to cast cards at any time and in any order, but still get a bonus from other cards interacting with the card(s) being cast. This sort of synergy will naturally be most beneficial with the use of permanents.