Broken is when a card is so powerful that it breaks one of the most traditional goal of a format is supposed to be, variety. Essentially, a broken card warps the format around itself demanding that it make a big impact on it. This can come in the manner of a card being in several different archetypes, or making their own archetype commonly played, at a high level, for an extensive period of time.
Now, Furretftw has made the point that every deck (or almost at least), absolutely needs energy, and that they all work around them. This however, was obviously intentional, pokemon have attacks, and they require energy, it's as basic as drawing a card each turn, and under such consideration, instead of being considered broken, or format warping, should be considered part of the intended design of pokemon.
It does not end there though, there are even other cards that have become such a basic part of decks that it is merely a fundamental development. Examples are Claydol, Roseanne's, Bebe's, Rare Candy, Uxie, Azelf, Night Maintenance, etc. It is true there are some decks that don't use these cards, but they are more than often an exception, and have something in place of these cards, the idea is still there, the cards are simply different. So there are powerful cards, that almost every deck needs to depend on, but, as a clearly intentional development, are not broken.
Now that we have defined what "Broken" is, let me list my own top 4, them being based on how warping they've become.
1) Luxray Gl
There is no question to this, currently appearing in the two top tier decks, hitting prices of $80 online, and making Speedrill powerful enough to take Worlds win last year. A truly broken trainer, brought back into the form of a pokemon Lv.X that can do 60 damage for one energy, and be online as early as T2. This card has become broken in both of the manners I listed, making it's own archetype widely playable, along with appearing in several archetypes.
2) SP Engine
I can not list the countless intuitive plays, and decisions to be made with such an amazing engine, letting some SP decks from needing the most basics of pokemon decks, alongside with creating a deadly array of adaptable answers to about any situation that can come up. The true threat behind all SP decks, this is certainly noteworthy.
3) Jumpluff
A true marvel in the current format, a stage 2 pokemon, with only 90hp, breaking into t4 tables worldwide. Racing at ridiculous speeds, for a stage 2 deck, it almost always gets the OHKO when it uses Mass Attack, and has another Jumpluff ready and waiting in the wings, expecting that Jumpluff to be knocked out. Essentially eliminating the need for a defensive altogether, Jumpluff is really extraordinary.
4) Crobat G
Often called the sophisticated man's plus power, this card, plus poketurns, appear in even more decks that Luxray GL, but at the same turn is not as impacting to games as said kitty. Ranging from key Gengar attacks (both old and new), to explosive Jumpluff Mass Attacks, to another tool for the sp engine to abuse, it definitely top dog among the backseat pokemon.