My two favorite pokemon quotes are in my signature but for the sake of starting things off here is another;
“…” ~ (as if this is even necessary) Red
Ha see what I did there! 
“Team rocket go bye bye?” said the last team rocket grunt who talked weird, leading to the others not telling him team rocket disbanded CX
You completed your Pokedex! Congratulations!
Nono, you guys are totally missing it.
“Smell ya later!” - Gary Oak.
How could we forget that? ;D
Good one,
What about “Don’t touch the poster at the Game Corner! There’s no secret switch behind it!” Rocket grunt from game corner (RBY)
Pretty much anything and everything that Lovrina from Pokemon XD says is my favorite. Maybe it’s the generic speech pattern, using “Oh so” in almost all of her sentences.
…You ninja me, even on forums.
You should be a teacher in ninja school. :c.
Oh and the most annoying sentence is:
Ill teach you how to catch a pokemon…
Most annoying and boring moment in pokemon games ._.
Uhg I hated that What about,
“This is my grandson, er what was his name?”
This… 
pfft~ u guys missing the point u cant forget…
“IF ur late ill fine u 100,000,000,000!!!”
barry from p/d/pt :'D they made me laugh because i was going to have to use debt
Back then in 1996 a girl said: “All this pokemon are so thin, I wish there was a pink, chubby one with flower patterns!”
16 years later, boom, Munna!
Lol but hey that’s what you get for sneaking up on the guy…
By the way I’m not sure if this is a full fledged quote but “It’s super effective!” is the best quote ever. Honestly try saying it next time you do something really cool.
Remember my super cool Rattata? My Rattata is different from regular Rattata. It’s like my Rattata is in the top percentage of Rattatas.
I’ll beat you with the Magikarp my dad gave me.
“I want to live in a world of games, anime, and comics forever.” - Maid Cyanea (Battle Subway)
“Meow, meow, it’s a battle, meow. (That sounds stupid, doesn’t it?) // Meowww… I lost, meowww. (Seriously, I am sooo embarrassed.)” - Waitress Terra (Battle Subway)
“I don’t want to go home, 'cause my wife is as scary as a legendary Pokémon.” - Worker Hayes (Battle Subway)
As you can see, I love battle subway quotes. >u>; xD
“Ugh, the Guildmaster’s a real special guy. Special in all sorts of ways…” ~ Loudred after one of the Guildmaster’s tantrums.
Pokemon Mystery Dungeons 2, Bidoof: Yup yup, yessir!
Everything Looker says. He seriously messes up every sentence, being foreign and all.
Gahhh fave quote is hard…
Well it might be “My rattata must be amongst the top percentage of rattata” Younger Joey we all saw it coming darlings~
i dunno if this counts, but
The foe’s blahblahblah used uberstrongmovethathasamissratewhichwilldearlycostmeapokemononmynuzlockes! The foe’s blahblahblah attack missed!
That moment of satisfaction and pleasure. Oh gosh.