I didn't really want to make a huge list, but dividing them by region isn't that helpful, what with the repeats. x_X
Kanto uses Gen I encounters (Red/Blue)
Johto uses Gen II encounters (Gold/Silver)
Hoenn uses Gen III encounters (Ruby/Sapphire)
Sinnoh uses Gen IV encounters (Diamond/Pearl)
Ferry Service available in either Vermilion City (Kanto), Olivine City (Johto), Slateport City (Hoenn) or Canalave City (Sinnoh).
Bailey, who can be found at the northern part of Route 104 (north of Petalburg Woods) in Hoenn.
Reed berry synthesis?Cherrygrove City (Johto)
http://vdexproject.net/map.php?place=fight_area Ada - Articuno - kanto -bottom level seafoam islands
Allen - Shaymin - White Flute to the Flower Paradise (which can be reached from Canalave if you have a Recommendation Letter).
Hari/Nao - Latias/Latios
Lyrit - Moltres
Rei - Rayquaza - HOENN -top of sky pillar
Zan - Cresselia - SINNOH - Fullmoon Island. You need an Aurora Ticket to get there from Canalave City; it's purchasable for $500 in any shop if you have the Lunar Wing. It'll roam after you try to catch it, and can be caught anywhere in the map afterward.
#001 #001 Bulbasaur
#002 #002 Ivysaur
#003 #003 Venusaur
#004 #004 Charmander
#005 #005 Charmeleon
#006 #006 Charizard
#007 #007 Squirtle
#008 #008 Wartortle
#009 #009 Blastoise
#010 #010 Caterpie
#011 #011 Metapod
#012 #012 Butterfree
#013 #013 Weedle
#014 #014 Kakuna
#015 #015 Beedrill
#016 #016 Pidgey
#017 #017 Pidgeotto
#018 #018 Pidgeot
#019 #019 Rattata
#020 #020 Raticate
#021 #021 Spearow
#022 #022 Fearow
#023 #023 Ekans
#024 #024 Arbok
#025 #025 Pikachu
#026 #026 Raichu
#027 #027 Sandshrew
#028 #028 Sandslash
#029 #029 Nidoran♀
#030 #030 Nidorina
#031 #031 Nidoqueen
#032 #032 Nidoran♂
#033 #033 Nidorino
#034 #034 Nidoking
#035 #035 Clefairy
#036 #036 Clefable
#037 #037 Vulpix
#038 #038 Ninetales
#039 #039 Jigglypuff
#040 #040 Wigglytuff
#041 #041 Zubat
#042 #042 Golbat
#043 #043 Oddish
#044 #044 Gloom
#045 #045 Vileplume
#046 #046 Paras
#047 #047 Parasect
#048 #048 Venonat
#049 #049 Venomoth
#050 #050 Diglett
#051 #051 Dugtrio
#052 #052 Meowth
#053 #053 Persian
#054 #054 Psyduck
#055 #055 Golduck
#056 #056 Mankey
#057 #057 Primeape
#058 #058 Growlithe
#059 #059 Arcanine
#060 #060 Poliwag
#061 #061 Poliwhirl
#062 #062 Poliwrath
#063 #063 Abra
#064 #064 Kadabra
#065 #065 Alakazam
#066 #066 Machop
#067 #067 Machoke
#068 #068 Machamp
#069 #069 Bellsprout
#070 #070 Weepinbell
#071 #071 Victreebel
#072 #072 Tentacool
#073 #073 Tentacruel
#074 #074 Geodude
#075 #075 Graveler
#076 #076 Golem
#077 #077 Ponyta
#078 #078 Rapidash
#079 #079 Slowpoke
#080 #080 Slowbro
#081 #081 Magnemite
#082 #082 Magneton
#083 #083 Farfetch'd
#084 #084 Doduo
#085 #085 Dodrio
#086 #086 Seel
#087 #087 Dewgong
#088 #088 Grimer
#089 #089 Muk
#090 #090 Shellder
#091 #091 Cloyster
#092 #092 Gastly
#093 #093 Haunter
#094 #094 Gengar
#095 #095 Onix
#096 #096 Drowzee
#097 #097 Hypno
#098 #098 Krabby
#099 #099 Kingler
#100 #100 Voltorb
#101 #101 Electrode
#102 #102 Exeggcute
#103 #103 Exeggutor
#104 #104 Cubone
#105 #105 Marowak
#106 #106 Hitmonlee
#107 #107 Hitmonchan
#108 #108 Lickitung
#109 #109 Koffing
#110 #110 Weezing
#111 #111 Rhyhorn
#112 #112 Rhydon
#113 #113 Chansey
#114 #114 Tangela
#115 #115 Kangaskhan
#116 #116 Horsea
#117 #117 Seadra
#118 #118 Goldeen
#119 #119 Seaking
#120 #120 Staryu
#121 #121 Starmie
#122 #122 Mr. Mime
#123 #123 Scyther
#124 #124 Jynx
#125 #125 Electabuzz
#126 #126 Magmar
#127 #127 Pinsir
#128 #128 Tauros
#129 #129 Magikarp
#130 #130 Gyarados
#131 #131 Lapras
#132 #132 Ditto
#133 #133 Eevee
#134 #134 Vaporeon
#135 #135 Jolteon
#136 #136 Flareon
#137 #137 Porygon
#138 #138 Omanyte
#139 #139 Omastar
#140 #140 Kabuto
#141 #141 Kabutops
#142 #142 Aerodactyl
#143 #143 Snorlax
#144 #144 Articuno
#145 #145 Zapdos
#146 #146 Moltres
#147 #147 Dratini
#148 #148 Dragonair
#149 #149 Dragonite
#150 #150 Mewtwo
#151 #151 Mew
#152 #152 Chikorita
#153 #153 Bayleef
#154 #154 Meganium
#155 #155 Cyndaquil
#156 #156 Quilava
#157 #157 Typhlosion
#158 #158 Totodile
#159 #159 Croconaw
#160 #160 Feraligatr
#161 #161 Sentret
#162 #162 Furret
#163 #163 Hoothoot
#164 #164 Noctowl
#165 #165 Ledyba
#166 #166 Ledian
#167 #167 Spinarak
#168 #168 Ariados
#169 #169 Crobat
#170 #170 Chinchou
#171 #171 Lanturn
#172 #172 Pichu
#173 #173 Cleffa
#174 #174 Igglybuff
#175 #175 Togepi
#176 #176 Togetic
#177 #177 Natu
#178 #178 Xatu
#179 #179 Mareep
#180 #180 Flaaffy
#181 #181 Ampharos
#182 #182 Bellossom
#183 #183 Marill
#184 #184 Azumarill
#185 #185 Sudowoodo
#186 #186 Politoed
#187 #187 Hoppip
#188 #188 Skiploom
#189 #189 Jumpluff
#190 #190 Aipom
#191 #191 Sunkern
#192 #192 Sunflora
#193 #193 Yanma
#194 #194 Wooper
#195 #195 Quagsire
#196 #196 Espeon
#197 #197 Umbreon
#198 #198 Murkrow
#199 #199 Slowking
#200 #200 Misdreavus
#201 #201 Unown
#202 #202 Wobbuffet
#203 #203 Girafarig
#204 #204 Pineco
#205 #205 Forretress
#206 #206 Dunsparce
#207 #207 Gligar
#208 #208 Steelix
#209 #209 Snubbull
#210 #210 Granbull
#211 #211 Qwilfish
#212 #212 Scizor
#213 #213 Shuckle
#214 #214 Heracross
#215 #215 Sneasel
#216 #216 Teddiursa
#217 #217 Ursaring
#218 #218 Slugma
#219 #219 Magcargo
#220 #220 Swinub
#221 #221 Piloswine
#222 #222 Corsola
#223 #223 Remoraid
#224 #224 Octillery
#225 #225 Delibird
#226 #226 Mantine
#227 #227 Skarmory
#228 #228 Houndour
#229 #229 Houndoom
#230 #230 Kingdra
#231 #231 Phanpy
#232 #232 Donphan
#233 #233 Porygon2
#234 #234 Stantler
#235 #235 Smeargle
#236 #236 Tyrogue
#237 #237 Hitmontop
#238 #238 Smoochum
#239 #239 Elekid
#240 #240 Magby
#241 #241 Miltank
#242 #242 Blissey
#243 #243 Raikou
#244 #244 Entei
#245 #245 Suicune
#246 #246 Larvitar
#247 #247 Pupitar
#248 #248 Tyranitar
#249 #249 Lugia Silver Wing to the deepest part of Whirlwind Islands
#250 #250 Ho-Oh
#251 #251 Celebi
#252 #252 Treecko
#253 #253 Grovyle
#254 #254 Sceptile
#255 #255 Torchic
#256 #256 Combusken
#257 #257 Blaziken
#258 #258 Mudkip
#259 #259 Marshtomp
#260 #260 Swampert
#261 #261 Poochyena
#262 #262 Mightyena
#263 #263 Zigzagoon
#264 #264 Linoone
#265 #265 Wurmple
#266 #266 Silcoon
#267 #267 Beautifly
#268 #268 Cascoon
#269 #269 Dustox
#270 #270 Lotad
#271 #271 Lombre
#272 #272 Ludicolo
#273 #273 Seedot
#274 #274 Nuzleaf
#275 #275 Shiftry
#276 #276 Taillow
#277 #277 Swellow
#278 #278 Wingull
#279 #279 Pelipper
#280 #280 Ralts
#281 #281 Kirlia
#282 #282 Gardevoir
#283 #283 Surskit
#284 #284 Masquerain
#285 #285 Shroomish
#286 #286 Breloom
#287 #287 Slakoth
#288 #288 Vigoroth
#289 #289 Slaking
#290 #290 Nincada
#291 #291 Ninjask
#292 #292 Shedinja
#293 #293 Whismur
#294 #294 Loudred
#295 #295 Exploud
#296 #296 Makuhita
#297 #297 Hariyama
#298 #298 Azurill
#299 #299 Nosepass
#300 #300 Skitty
#301 #301 Delcatty
#302 #302 Sableye
#303 #303 Mawile
#304 #304 Aron
#305 #305 Lairon
#306 #306 Aggron
#307 #307 Meditite
#308 #308 Medicham
#309 #309 Electrike
#310 #310 Manectric
#311 #311 Plusle
#312 #312 Minun
#313 #313 Volbeat
#314 #314 Illumise
#315 #315 Roselia
#316 #316 Gulpin
#317 #317 Swalot
#318 #318 Carvanha
#319 #319 Sharpedo
#320 #320 Wailmer
#321 #321 Wailord
#322 #322 Numel
#323 #323 Camerupt
#324 #324 Torkoal
#325 #325 Spoink
#326 #326 Grumpig
#327 #327 Spinda
#328 #328 Trapinch
#329 #329 Vibrava
#330 #330 Flygon
#331 #331 Cacnea
#332 #332 Cacturne
#333 #333 Swablu
#334 #334 Altaria
#335 #335 Zangoose
#336 #336 Seviper
#337 #337 Lunatone
#338 #338 Solrock
#339 #339 Barboach
#340 #340 Whiscash
#341 #341 Corphish
#342 #342 Crawdaunt
#343 #343 Baltoy
#344 #344 Claydol
#345 #345 Lileep
#346 #346 Cradily
#347 #347 Anorith
#348 #348 Armaldo
#349 #349 Feebas
#350 #350 Milotic
#351 #351 Castform
#352 #352 Kecleon
#353 #353 Shuppet
#354 #354 Banette
#355 #355 Duskull
#356 #356 Dusclops
#357 #357 Tropius
#358 #358 Chimecho
#359 #359 Absol
#360 #360 Wynaut
#361 #361 Snorunt
#362 #362 Glalie
#363 #363 Spheal
#364 #364 Sealeo
#365 #365 Walrein
#366 #366 Clamperl
#367 #367 Huntail
#368 #368 Gorebyss
#369 #369 Relicanth
#370 #370 Luvdisc
#371 #371 Bagon
#372 #372 Shelgon
#373 #373 Salamence
#374 #374 Beldum
#375 #375 Metang
#376 #376 Metagross
#377 #377 Regirock
#378 #378 Regice
#379 #379 Registeel
#380 #380 Latias
#381 #381 Latios
#382 #382 Kyogre
#383 #383 Groudon
#384 #384 Rayquaza
#385 #385 Jirachi
#386 #386 Deoxys
#387 #387 Turtwig
#388 #388 Grotle
#389 #389 Torterra
#390 #390 Chimchar
#391 #391 Monferno
#392 #392 Infernape
#393 #393 Piplup
#394 #394 Prinplup
#395 #395 Empoleon
#396 #396 Starly
#397 #397 Staravia
#398 #398 Staraptor
#399 #399 Bidoof
#400 #400 Bibarel
#401 #401 Kricketot
#402 #402 Kricketune
#403 #403 Shinx
#404 #404 Luxio
#405 #405 Luxray
#406 #406 Budew
#407 #407 Roserade
#408 #408 Cranidos
#409 #409 Rampardos
#410 #410 Shieldon
#411 #411 Bastiodon
#412 #412 Burmy
#413 #413 Wormadam
#414 #414 Mothim
#415 #415 Combee
#416 #416 Vespiquen
#417 #417 Pachirisu
#418 #418 Buizel
#419 #419 Floatzel
#420 #420 Cherubi
#421 #421 Cherrim
#422 #422 Shellos
#423 #423 Gastrodon
#424 #424 Ambipom
#425 #425 Drifloon
#426 #426 Drifblim
#427 #427 Buneary
#428 #428 Lopunny
#429 #429 Mismagius
#430 #430 Honchkrow
#431 #431 Glameow
#432 #432 Purugly
#433 #433 Chingling
#434 #434 Stunky
#435 #435 Skuntank
#436 #436 Bronzor
#437 #437 Bronzong
#438 #438 Bonsly
#439 #439 Mime Jr.
#440 #440 Happiny
#441 #441 Chatot
#442 #442 Spiritomb
#443 #443 Gible
#444 #444 Gabite
#445 #445 Garchomp
#446 #446 Munchlax
#447 #447 Riolu
#448 #448 Lucario
#449 #449 Hippopotas
#450 #450 Hippowdon
#451 #451 Skorupi
#452 #452 Drapion
#453 #453 Croagunk
#454 #454 Toxicroak
#455 #455 Carnivine
#456 #456 Finneon
#457 #457 Lumineon
#458 #458 Mantyke
#459 #459 Snover
#460 #460 Abomasnow
#461 #461 Weavile
#462 #462 Magnezone
#463 #463 Lickilicky
#464 #464 Rhyperior
#465 #465 Tangrowth
#466 #466 Electivire
#467 #467 Magmortar
#468 #468 Togekiss
#469 #469 Yanmega
#470 #470 Leafeon
#471 #471 Glaceon
#472 #472 Gliscor
#473 #473 Mamoswine
#474 #474 Porygon-Z
#475 #475 Gallade
#476 #476 Probopass
#477 #477 Dusknoir
#478 #478 Froslass
#479 #479 Rotom
#480 #480 Uxie Red Chain to Acuity Cave
#481 #481 Mesprit Red Chain to Verity Cave
#482 #482 Azelf
#483 #483 Dialga
#484 #484 Palkia
#485 #485 Heatran Magma Rock to the deepest part of Stark Mountain
#486 #486 Regigigas
#487 #487 Giratina
#488 #488 Cresselia
#489 #489 Phione
#490 #490 Manaphy
#491 #491 Darkrai Member Card to Newmoon Island. You need a Mystic Ticket to get there from Canalave City; it's purchasable for $500 in any shop if you have the Member Card.
#492 #492 Shaymin
#493 #493 Arceus