So way back in 2003, we were introduced to Pokémon-ex in the set EX: Ruby & Sapphire. Give or take the odd promo, I think the last of these were released in EX: Power Keepers in 2007. They were a new rarity back then, one step above holographic rare. They had rules text on them stating they gave up an extra Prize when KO'd. They could be Basic, Stage 1, or Stage 2 Pokémon, and if they were an Evolution, most Evolved from the same lower Stage as the non-Pokémon-ex version of the card. For example, Jolteon-ex was a Stage 1 that Evolved from Eevee, though there were oddballs like Scizor-ex that could Evolve from the regular Scyther or Scyther-ex. Probably because they bothered to make a Scyther-ex.
Pokémon-EX were first introduced in BW: Next Destinies in 2012 and didn't stop being released until... actually they are still releasing a few Alternate Printings of them now, though I think new ones were done with either XY: Evolutions or the last of the XY: Black Star Series. They are also worth two Prizes when KO'd, but are either Basic Pokémon (even if the Pokémon in question is normally a different Stage) or Mega Evolutions. At first, only Pokémon that - in the video games - are described as Legendaries would get Pokémon-EX, but soon it seemed to be whatever the designers felt like.
The newest gimmick is Pokémon-GX. Again, they are worth an extra Prize when KO'd. They debuted in the SM: Black Star Promos series with Snorlax-GX last year. They all have three effects; an Ability and two attacks, or three attacks, and one of the attacks is a GX-attack that can only be used once during a game. They can be any Stage still in use for the Sun & Moon era, and Evolve from the non-Pokémon-GX version of their prior Stage. For example, Umbreon-GX Evolves from Eevee.
For the 4-copy rule, all these cards are considered to have different names. Effects that refer to Pokémon-ex do not apply to Pokémon-EX, and vice versa. Effects that refer to Pokémon-EX do not apply to Pokémon-GX, and vice versa. There are, however, some effects that specifically state they apply to both Pokémon-EX and Pokémon-GX, like the damage boost from Choice Band.