Note:  If an area is not listed, assume the same encounters as vanilla Emerald

=Route 101=
Grass:
-Zigzagoon (45%)
-Poochyena (45%)
-Pidgey (5%)
-Sentret (5%)

=Route 102=
Grass:
-Zigzagoon (40%)
-Poochyena (40%)
-Ledyba (10%)
-Ratatta (5%)
-Ralts (4%)
-Surskit (1%)
Fishing:
-Poliwag (Old Rod, 70%) (Good Rod, 60%)
-Goldeen (Old Rod, 30%) (Good Rod, 20%)
-Corphish (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Marill (60%)
-Poliwag (35%)
-Goldeen (4%)
-Surskit (1%)

=Route 103=
Grass:
-Zigzagoon (40%)
-Poochyena (40%)
-Wingull (10%)
-Ratatta (5%)
-Ledyba (5%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 104=
Grass:
-Taillow (35%)
-Wingull (35%)
-Marill (20%)
-Spinarak (5%)
-Hoothoot (5%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%) (Super Rod, 75%)
-Wooper (Old Rod, 30%) (Good Rod, 40%) (Super Rod, 25%)
-Quagsire (Super Rod, 5%)

=Route 105=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Qwilfish (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Route 106=
Fishing:
-Magikarp (Old Rod, 100%) (Good Rod, 60%)
-Qwilfish (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Route 107=
Fishing:
-Magikarp (Old Rod, 100%) (Good Rod, 60%)
-Qwilfish (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Route 108=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Qwilfish (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Route 109=
Fishing:
-Magikarp (Old Rod, 100%) (Good Rod, 60%)
-Qwilfish (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Route 110=
Grass:
-Electrike (30%)
-Oddish (25%)
-Gulpin (20%)
-Plusle (10%)
-Minun (10%)
-Mareep (5%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 111=
Desert:
-Trapinch (40%)
-Sandshrew (35%)
-Diglett (18%)
-Cacnea (5%)
-Larvitar (2%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Barboach (Old Rod, 30%) (Good Rod, 40%) (Super Rod, 100%)
Surfing:
-Marill (99%)
-Goldeen (1%)

=Route 112=
Grass:
-Nidoran M (35%)
-Nidoran F (35%)
-Ekans (20%)
-Meowth (5%)
-Growlithe (5%)

=Route 113=
Grass:
-Spinda (50%)
-Slugma (30%)
-Skarmory (10%)
-Ponyta (5%)
-Houndour (5%)

=Route 114=
Grass:
-Swablu (40%)
-Lotad (30%)
-Lombre (10%)
-Seviper (10%)
-Zangoose (10%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Wooper (Old Rod, 30%) (Good Rod, 20%) (Super Rod, 30%)
-Barboach (Good Rod, 20%) (Super Rod, 70%)
Surfing:
-Marill (95%)
-Goldeen (4%)
-Surskit (1%)

=Route 115=
Grass:
-Taillow (40%)
-Swablu (25%)
-Drowzee (15%)
-Jigglypuff (15%)
-Swellow (5%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Snorlax (only one, must use Surf)

=Route 116=
Grass:
-Poochyena (35%)
-Taillow (25%)
-Nincada (25%)
-Abra (10%)
-Skitty (4%)
-Snubbull (1%)

=Route 117=
Grass:
-Bellsprout (40%)
-Volbeat (20%)
-Illumise (20%)
-Roselia (15%)
-Seedot (5%)
Fishing:
-Poliwag (Old Rod, 70%) (Good Rod, 60%)
-Corphish (Old Rod, 30%) (Good Rod, 40%) (Super Rod, 100%)
Surfing:
-Marill (95%)
-Goldeen (4%)
-Surskit (1%)

=Route 118=
Grass:
-Hoppip (30%)
-Electrike (30%)
-Wingull (19%)
-Skiploom (10%)
-Manectric (10%)
-Kecleon (1%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Carvanha (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 119=
Grass:
-Tangela (30%)
-Zigzagoon (30%)
-Linoone (30%)
-Tropius (9%)
-Kecleon (1%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Carvanha (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Feebas (Any rod 50%, appears in 6 tiles)
-Kecleon (only two)
-Castform (Weather Institute)

=Route 120=
Grass:
-Furret (30%)
-Tangela (25%)
-Sentret (20%)
-Marill (15%)
-Absol (8%)
-Kecleon (1%)
-Surskit (1%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Goldeen (Old Rod, 30%) (Good Rod, 20%) (Super Rod, 30%)
-Barboach (Good Rod, 20%) (Super Rod, 70%)
Surfing:
-Marill (99%)
-Surskit (1%)

=Route 121=
Grass:
-Shuppet (30%)
-Sentret (20%)
-Furret (20%)
-Bellsprout (15%)
-Gastly (9%)
-Weepinbell (5%)
-Kecleon (1%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Snorlax (only one)

=Route 122=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 123=
Grass:
-Shuppet (30%)
-Sentret (20%)
-Furret (20%)
-Bellsprout (15%)
-Gastly (9%)
-Weepinbell (5%)
-Keckleon (1%)
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 124=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 55%)
-Sharpedo (Super Rod, 40%)
-Seel (Super Rod, 5%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Pelipper (5%)
-Seel (4%)
-Dewgong (1%)
Underwater:
-Clamperl (60%)
-Chinchou (30%)
-Shellder (5%)
-Relicanth (5%)

=Route 125=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 126=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Underwater:
-Clamperl (60%)
-Chinchou (30%)
-Shellder (5%)
-Relicanth (5%)

=Route 127=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Lapras (only one, shiny)

=Route 128=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Luvdisc (Good Rod, 20%) (Super Rod, 40%)
-Corsola (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Route 129=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 55%)
-Sharpedo (Super Rod, 40%)
-Wailord (Super Rod, 5%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Pelipper (5%)
-Lapras (5%)

=Route 130=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 55%)
-Sharpedo (Super Rod, 40%)
-Wailord (Super Rod, 5%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Pelipper (5%)
-Lapras (5%)

=Route 131=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 55%)
-Sharpedo (Super Rod, 40%)
-Wailord (Super Rod, 5%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Pelipper (5%)
-Mantine (5%)

=Route 132=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 45%)
-Sharpedo (Super Rod, 40%)
-Horsea (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Mantine (10%)

=Route 133=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 45%)
-Sharpedo (Super Rod, 40%)
-Horsea (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Mantine (10%)

=Route 134=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 45%)
-Sharpedo (Super Rod, 40%)
-Horsea (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (30%)
-Mantine (10%)

=Petalburg City=
Fishing:
-Goldeen (Old Rod, 100%) (Good Rod, 80%)
-Corphish (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Marill (100%)

=Rustboro City=
Trade:
-Porygon (give Ralts)

=Dewford Town=
Fishing:
-Magikarp (Old Rod, 100%) (Good Rod, 60%)
-Qwilfish (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Slateport City=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Qwilfish (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 100%)
Surfing:
-Qwilfish (60%)
-Wingull (30%)
-Pelipper (10%)

=Verdanturf Town=
Other:
-Treecko/Torchic/Mudkip (purchased from egg seller)

=Lavaridge Town=
Other:
-Wynaut (egg from lady)
-Togepi (egg from lady after receiving Wynaut and beating Pokemon League, only one)

=Fortree City=
Trade:
-Eevee (give Skarmory)

=Lilycove City=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 85%)
-Staryu (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Chikorita/Cyndaquil/Totodile (purchased from egg seller)

=Mossdeep City=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Other:
-Jirachi (only one, must finish w/ Team Magma in Space Center)

=Pacifidlog Town=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Wailmer (Good Rod, 20%) (Super Rod, 60%)
-Sharpedo (Super Rod, 40%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)
Trade:
-Smoochum (give Bagon)

=Sootopolis City=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 100%) (Super Rod, 80%)
-Tentacool (Old Rod, 30%)
-Gyarados (Super Rod, 20%)
Surfing:
-Magikarp (100%)

=Ever Grande City=
Fishing:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%)
-Wailmer (Good Rod, 20%) (Super Rod, 45%)
-Luvdisc (Good Rod, 20%) (Super Rod, 40%)
-Corsola  (Super Rod, 15%)
Surfing:
-Tentacool (60%)
-Wingull (35%)
-Pelipper (5%)

=Battle Frontier=
Trade:
-Unown (give Xatu)
Other:
-Bulbasaur/Charmander/Squirtle (purchased from egg seller)
-Sudowoodo (only one)

=Petalburg Woods=
Grass:
-Wurmple (40%)
-Shroomish (35%)
-Weedle (10%)
-Caterpie (10%)
-Pineco (4%)
-Slakoth (1%)
Other:
-Celebi (only one, must have GS Ball)

=Rusturf Tunnel=
Cave:
-Whismur (85%)
-Zubat (15%))

=Granite Cave=
Cave, 1F:
-Zubat (45%)
-Makuhita (30%)
-Geodude (20%)
-Tyrogue (4%)
-Onix (1%)
Cave, B1:
-Zubat (40%)
-Aron (30%)
-Makuhita (14%)
-Mawile (10%)
-Sableye (5%)
-Onix (1%)
Cave, B2:
-Zubat (50%)
-Aron (34%)
-Sableye (10%)
-Mawile (5%)
-Onix (1%)
Cave, Steven's Room:
-Zubat (50%)
-Makuhita (30%)
-Aron (10%)
-Nosepass (10%)

=Mirage Tower=
Tower, 1F:
-Diglett (55%)
-Sandshrew (39%)
-Dugtrio (4%)
-Larvitar (2%)
Tower, 2F/3F/4F:
-Baltoy (35%)
-Trapinch (30%)
-Sandshrew (30%)
-Larvitar (5%)
Other:
-Omanyte/Kabuto/Aerodactyl/Lileep/Anorith fossils in Mirage Tower (pick 2 of 5, other 3 go to Desert Underpass)

=Fiery Path=
Cave:
-Numel (35%)
-Koffing (25%)
-Torkoal (25%)
-Grimer (10%)
-Magmar (5%)

=Meteor Falls=
Cave, 1F 1R:
-Zubat (50%)
-Lunatone (20%)
-Solrock (20%)
-Paras (8%)
-Clefairy (2%)
Fishing, 1F 1R:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Poliwag (Old Rod, 30%) (Good Rod, 20%) (Super Rod, 30%)
-Barboach (Good Rod, 20%) (Super Rod, 70%)
Surfing, 1F 1R:
-Zubat (90%)
-Solrock (5%)
-Lunatone (5%)
Cave, 1F 2R/B1 1R:
-Golbat (50%)
-Lunatone (20%)
-Solrock (20%)
-Parasect (8%)
-Clefairy (2%)
Fishing, 1F 2R:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Poliwag (Old Rod, 30%) (Good Rod, 20%) (Super Rod, 30%)
-Barboach (Good Rod, 20%) (Super Rod, 40%)
-Whiscash (Super Rod, 30%)
Surfing, 1F 2R/B1 1R/B1 2R:
-Golbat (90%)
-Solrock (5%)
-Lunatone (5%)
Cave, B1 2R:
-Golbat (53%)
-Lunatone (10%)
-Solrock (10%)
-Bagon (25%)
-Clefairy (2%)
Fishing, B1 1R/B1 2R:
-Magikarp (Old Rod, 70%) (Good Rod, 60%)
-Poliwag (Old Rod, 30%) (Good Rod, 20%) (Super Rod, 30%)
-Barboach (Super Rod, 40%)
-Whiscash (Super Rod, 15%)
-Dratini (Good Rod, 20%) (Super Rod, 10%)
-Dragonair (Super Rod, 5%)

=Jagged Pass=
Grass:
-Numel (40%)
-Machop (30%)
-Spoink (20%)
-Spearow (5%)
-Mankey (5%)

=New Mauville=
Interior, 1F/B1:
-Magnemite (44%)
-Voltorb (44%)
-Grimer (10%)
-Electabuzz (2%)
Other:
-Zapdos (only one)

=Safari Zone=
Grass, Area 1:
-Exeggcute (40%)
-Doduo (30%)
-Girafarig (15%)
-Pikachu (8%)
-Scyther (7%)
Grass, Area 2:
-Exeggcute (35%)
-Venonat (30%)
-Natu (20%)
-Pikachu (10%)
-Mr. Mime (5%)
Fishing, Area 2/Area 3:
-Slowpoke (Old Rod, 70%) (Good Rod, 60%)
-Psyduck (Old Rod, 30%) (Good Rod, 40%) (Super Rod, 70%)
-Dratini (Super Rod, 25%)
-Dragonair (Super Rod, 5%)
Surfing, Area 2/Area 3:
-Slowpoke (90%)
-Dratini (9%)
-Dragonair (1%)
Grass, Area 3:
-Natu (30%)
-Rhyhorn (30%)
-Sunkern (25%)
-Teddiursa (10%)
-Pinsir (5%)
Grass, Area 4:
-Natu (35%)
-Rhyhorn (30%)
-Phanpy (25%)
-Heracross (8%)
-Chansey (2%)
Other, Area 4:
-Shuckle (Rock Smash, 95%)
-Dunsparce (Rock Smash, 5%)
Grass, Area 5:
-Aipom (30%)
-Gligar (30%)
-Farfetch'd (25%)
-Stantler (10%)
-Kangaskhan (5%)
Fishing, Area 5:
-Krabby (Old Rod, 70%) (Good Rod, 60%) (Super Rod, 40%)
-Remoraid (Old Rod, 30%) (Good Rod, 40%) (Super Rod, 55%)
-Octillary (Super Rod, 5%)
Surfing, Area 5:
-Krabby (60%)
-Remoraid (35%)
-Octillery (5%)
Grass, Area 6:
-Gligar (30%)
-Yanma (25%)
-Aipom (20%)
-Miltank (10%)
-Tauros (10%)
-Lickitung (5%)
Other, Area 6:
-Shuckle (Rock Smash, 95%)
-Dunsparce (Rock Smash, 5%)

=Mt. Pyre=
Interior, 1F/2F/3F:
-Shuppet (65%)
-Gastly (15%)
-Misdreavus (15%)
-Cubone (5%)
Interior, 4F/5F/6F:
-Shuppet (65%)
-Gastly (15%)
-Duskull (15%)
-Haunter (5%)
Grass, Exterior:
-Vulpix (30%)
-Meditite (30%)
-Misdreavus (25%)
-Murkrow (15%)
Grass, Summit:
-Shuppet (70%)
-Duskull (14%)
-Gastly (14%)
-Chimecho (2%)

=Magma Hideout=
Cave, All Rooms:
-Geodude (50%)
-Torkoal (30%)
-Graveller (15%)
-Onix (5%)

=Shoal Cave=
Main Cave, Both Tides:
-Spheal (45%)
-Zubat (40%)
-Krabby (10%)
-Golbat (5%)
Fishing:
-Krabby (Old Rod, 70%) (Good Rod, 60%)
-Tentacool (Old Rod, 30%) (Good Rod, 20%)
-Seel (Good Rod, 20%) (Super Rod, 95%)
-Dewgong (Super Rod, 5%)
Surfing:
-Tentacool (60%)
-Zubat (30%)
-Seel (10%)
Ice Floor, Low Tide:
-Swinub (55%)
-Delibird (33%)
-Snorunt (10%)
-Sneasel (2%)
Other:
-Articuno (only one, must be low tide)

=Sky Pillar=
Interior, 1F/3F:
-Golbat (30%)
-Sableye (25%)
-Mawile (25%)
-Claydol (15%)
-Wobbuffet (5%)
Interior, 5F:
-Golbat (30%)
-Sableye (25%)
-Mawile (25%)
-Claydol (15%)
-Altaria (5%)
Other:
-Rayquaza (only one, after Sootopolis)

=Victory Road=
Other:
-Moltres (only one)

=Altering Cave=
Cave:
-Zubat (90%)
-Wobbuffet (10%)
Other:
-Mewtwo (only one, must beat the Elite Four)

=Desert Underpass=
Cave:
-Ditto (50%)
-Diglett (34%)
-Dugtrio (16%)
Other:
-Omanyte/Kabuto/Aerodactyl/Lileep/Anorith fossils in Mirage Tower (the 3 which were not taken in Mirage Tower)

=Artisan Cave=
Cave:
-Smeargle (100%)

=Other=
Roaming:
-Groudon (after Sootopolis)
-Kyogre (after Sootopolis)
-Lati@s (choose one after beating Elite Four)
-Raikou (after chosen Lati)
-Entei (after Raikou)
-Suicune (after Entei)
Southern Island:
-Non-roaming Lati@s (get Eon Ticket in Mossdeep from the old guy at the south end of the city after the E4)
Birth Island:
-Deoxys (get AuroraTicket from scientst in Space Center after meteor crash)
Naval Rock:
-Lugia (get MysticTicket from Scott after obtaining a set of Silver Symbols at the Battle Frontier)
-Ho-Oh ("")
Faraway Island:
-Mew (get Old Sea Map from the Sailor at Slateport by the shipyard after E4)