Milotic - got the Feebas back in Pokémon Black after a few days of hunting, then traded it to my White and back again. Even though it doesn't have the best nature or IVs, I still use it for competitive battling.
Scolipede - 100% competitive battle ready and hatched for me by one of my friends who breeds like crazy. 5/6 IVs (the missing one is SpA).
Clawitzer - got the Clauncher after a fishing chain of 2 in X just to test how chain fishing worked. It was the shiny I wanted, too!
Terrakion - got this from a guy on Pokémon Showdown, 6/6 IVs and a perfect nature. Dunno if it's legit or not, but I haven't seen his OT on the list of people with known cheated OTs. Even though it's perfect, I rarely use it in competitive battles.
Tyranitar - got this from the same friend who bred the Scolipede.
Hydreigon (x2) - got the first one after about a week and a half of searching in Black, but it had a terrible nature so I never used it except as a trophy. Then my friend bred me a new, 100% battle ready one that I use all the time.
Deoxys - had a friend who managed to grab a copy of Emerald with the Deoxys event ticket on it as well as the Mew event ticket, so I SR'd roughly 20000 times for the Deoxys.
Genesect - nothing special here, just the Korean event one.
Steelix - bred for me by my breeding friend.
Audino (x2) - found the first one when I was grinding EXP off Audinos in Black. Got the second from my breeding friend who bred an extra one and gave it to me for winning a tournament he hosted for all of our friends that play Pokémon.
Gyarados - just the one from HG/SS, nothing special.
Riolu - bred it myself but never got around to doing anything with it.
Darkrai - almost certain this one is cheated. I actually forget that I have it sometimes.
Dialga - SR'd for about a week in Diamond.
Chandelure - got it in Black after about a month (!) of searching in that one tower.
Zorua - accidentally bred it while breeding for a competitive Zoroark. Never got around to doing anything with it.
Gengar (x3) - found one in Giratina's cave in Pearl. The other two are Fall 2014 event ones.
Pawniard - found it in my cousin's Friend Safari while hunting for an HA Crawdaunt.
Gallade - no idea where the hell it came from. I just kinda have it, like my Darkrai.
Latios - managed to get it in my old Ruby cartridge because I never caught it, so I decided to shiny hunt for it. Wish I could've waited for OrAs.
Volcarona - came from my White after a LOT of SRs.
Tepig - bred it in Black intending to do a shiny starter only run but never got around to it.
Kyogre - came from my Japanese Sapphire cartridge which unfortunately stopped working.
Beldum - from the OrAs event.
Metagross - also from the OrAs event.
Snivy - bred for the same purpose as the Tepig, now sits unused.
Dratini (x2) - one from White 2, the other from breeding.
Raichu - from some North American event, forgot which one.
Woobat - from one of my friends who wanted it for one of my spare shiny event legendaries (I think it was one of my spare Raikous).
Raikou (x2) - from the event.
Entei (x3) - from the event.
Suicune (x3) - from the event.
Rhyperior - found it randomly in my Diamond game as a Rhydon, then traded it and traded it back.
Leafeon - bred in my Black game, decided to evolve it into Leafeon because I like Leafeon.
Claydol - found it in my old Ruby.
Gigalith - got it from the GTS since I was too lazy to find one myself. Got it immediately.
Rufflet - bred it in Black, don't remember why.
Camerupt - it's definitely hacked, without a doubt. Got it from someone on Pokémon Showdown.
Zigzagoon - found while EV training in AS.
Ho-oh - got it from the GTS back in Pearl because I wanted it and I didn't realize there were remakes on the way because they hadn't been announced.
Lugia - same deal as Ho-oh.
Gastrodon - found it with the PokéRadar in Pearl.
Lopunny - found the Buneary with the PokéRadar in Pearl.
Ludicolo - don't know where the hell I got it. I just have it.
ing lot from when I constantly used Action Replay, Red Gyrados from SoulSilver, 2 of each of the Gen IV box art legendaries from the Gen V event, Garchomp from Black 2, and the Marill from AS. Not sure if there were any others.
