001 - Bulbasaur [PHL2] [Rage candybar, I think]
002 - Ivysaur [PHL2]

004 - Charmander [PHL2]
005 - Charmeleon [PHL2]
006 - Charizard [PHL2]

021 - Spearow [PHL2]
022 - Fearow [PHL2]

032 - Nidoran♂ [PHL2] [Caught in Viridian (or nearby)]
033 - Nidorino [PHL2]
034 - Nidoking [PHL2]

129 - Magikarp [PHL2] [Received from Jimmy]
130 - Gyarados [PHL2]

135 - Jolteon [PHL2, first horoscope]

138 - Omanyte - Revived at Cinnabar

140 - Kabuto - Revived at Cinnabar

142 - Aerodactyl [PHL2] [Caught from Incense]

194 - Wooper [PHL2] [Johto]

198 - Murkrow [PHL2] [Caught from Incense]

200 - Misdreavus [PHL2] [Received from Leon for Noibat]

207 - Gligar [PHL2] [Traded to Rose]

227 - Skarmory [PHL2] [Caught from Incense, traded to Rose for Bagon]
228 - Houndour - Caught at Lake Valor
229 - Houndoom - Evolved at Lake Valor

238 - Smoochum [PHL2] [Received from Jimmy]

255 - Torchic
258 - Mudkip [PHL2] [Horoscope]
259 - Marshtomp [PHL2]
260 - Swampert [PHL2]

280 - Ralts [PHL2] [Received from Jimmy]
281 - Kirlia [PHL2] [Evolved in Laverre?]

337 - Anorith - Revived at Cinnabar

371 - Bagon [PHL2] [Received from Rose]

374 - Beldum [PHL2] [Received from Jimmy]
375 - Metang [PHL2]
376 - Metagross [PHL2]

386 - Deoxys [PHL2] [Pingo]
390 - [utl=http://www.gaiaonline.com/guilds/viewtopic.php?page=1&t=24796783#374015477]Chimchar

410 - Shieldon - Revived at Cinnabar

458 - Mantyke [PHL2] [Caught from Incense]

566 - Archen [PHL2] [Caught from Incense]

571 - Zoroark [PHL2] [Christmas Event?]

580 - Ducklett [PHL2] [Caught from Incense]

595 - Joltik [PHL2] [Halloween Giveaway]

633 - Deino [PHL2] [Halloween Event]

653 - Fennekin from Kail received originally through Easter event

674 - Pancham [PHL2] [Received from Rose, for Gligar?]

707 - Klefki - Caught in Lost Hotel

714 - Noibat [PHL2] [Caught from Incense, traded to Leon]