Elite Pokemon are a recent addition. The Poke will appear and say 'An Elite Pokemon has appeared' and the Poke will have an [E] in front of it's name. These Pokemon are much stronger than regular wild Pokes, so don't take them lightly. They are also much harder to catch, so I wouldn't bother trying unless you are unfortunate enough to meet a [E]rare. Either way, catch or K.O., they will always drop something. I think it's odds of 1/5 or something that they'll drop an Elite Token(in your bag it'll be a little light blue coin) which is what you're wanting.You can use these these at the Elite Shop by talking to Lance in the Indigo Plateau. Other drops include potions, EV Resets, any of the special Pokeballs introduced in gen 2(Repeat Ball, Level Ball, Nest Ball, Fast Ball, ect.)If you don't know what I'm talking about here's a list of the special Pokeballs.