I quite messy with my place anotations but here are my anotations:
Pallet Town(4)
x Right next to Raichu's Tower (<<).
x Right next to Raichu's Tower (STAIRS) (>>)
x North of Ash's House, at stairs: Position: {x = 3529, y = 3513, z = 5}.
x Next to Delia's Ketchum House
Viridian(9)
x Mankeys
x
Position: {x = 3469, y = 3272, z = 7}.
x Snorlax's Spawn
x South of PC
x Viridian last upstairs at colliseum <
x Viridian Forest - NPC Harold
x Viridian Forest - NPC Harold x2
x At Bulbasaur Spawn
x Single Wartortle Spawn
Pewter(7)
x
Position: {x = 3556, y = 3447, z = 5}.
x
Position: {x = 3533, y = 2997, z = 6}.
x West from Town: Position: {x = 3447, y = 3344, z = 5}.
x Juanito >
x Pewter Quest Entrance: Position: {x = 3295, y = 3037, z = 7}.
x Pewter Train Station
x
Position: {x = 3437, y = 3058, z = 6}.
Cerulean(10)
x >>>> cidade navio
x West Entrance
x West Entrance x2
x Cerulean Beach
Position: {x = 3851, y = 2905, z = 7}.
x At Diglets (>>): Position: {x = 4019, y = 2887, z = 6}.
x On a "Cubone-Head Cave" before Tower Quest (Marowaks), enter there and go to the south.
x From Marowak Quest, to the south, on the border of the map - Position: {x = 3946, y = 2993, z = 6}.
x Near Digglets
Position: {x = 3927, y = 3001, z = 7}.
x Cerulean Onix's Spawn (need rock Smash)
x Bill >
12:23 You see Kinder surprise egg.
Position: {x = 3890, y = 2900, z = 8}.
Saffron(2)
x Top of a Building near the East entrance (can be seen on the picture)
x Saffron sewer
Celadon(11)
x
Position: {x = 3916, y = 3176, z = 7}.
x Mt. Moon Entrance (Jigglypuff)
x Mt. Moon x2 (Signle Clefairy)
x Team Rocket's Hideout.
x At Celadon's Church (North-East)
x Top of Celadon's Big Market
x At the Parasect right behind Celadon's Big Market
x At Gastly's Spot (north of Celadon)
x Muk Single Spawn at Sewers (Where you buy parcels)
x At the beach, near CP
x Celadon >
Position: {x = 3818, y = 3254, z = 7}
Vermillion(5)
x Before Gengar stairs at the Gastly "Camp" (>>)
x Below Burning House
Position: {x = 3916, y = 3306, z = 7}.
x Near Burning House
Position: {x = 3916, y = 3306, z = 7}.
x Near Burning House(x2)
Position: {x = 3886, y = 3292, z = 7}.
x Near the boat (<<).
Position: {x = 3841, y = 3337, z = 7}.
Lavender(6)
x
Position: {x = 3912, y = 3271, z = 7}.
x Inside Rock tunnel <
x Near Thunder Plant
Position: {x = 3975, y = 3087, z = 7}.
x
Position: {x = 4058, y = 3278, z = 7}.
x North East of Lavender, at Gastly's Spawn
x Near dugtrio task npc
Fuchsia(12)
x Saffari
x Next to Adolph (South of PC)
x Daycare
x Dodrio's Spawn
x East from Dodrio's Spawn (>>)
Position: {x = 3956, y = 3538, z = 7}.
x East from Dodrio's Spawn (>>) (x2)
Position: {x = 3967, y = 3521, z = 6}.
x Same as ^, but where the Geodude's are.
x Fuchsia Venom Quest
x
Position: {x = 3913, y = 3370, z = 7}.
x
Position: {x = 3906, y = 3411, z = 7}.
x
Position: {x = 3961, y = 3418, z = 7}.
x North from Fuchsia Venom Quest: Position: {x = 4003, y = 3432, z = 7}.
Cinnabar(5)
x sewer cinnabar
x
Position: {x = 3434, y = 3779, z = 7}.
x
Position: {x = 3358, y = 3676, z = 4}.
x West from PC
x North West from PC: Position: {x = 3357, y = 3639, z = 7}.
Johto Region
x
Position: {x = 2840, y = 4682, z = 5}.
Cianwood(3)
x Entrance of Yellow Hall Quest (at Town)
x Yellow Hall Quest
x Behind Janito
Azalea(7)
x Black Market
x
Position: {x = 2760, y = 4765, z = 8}.
x At the Shop.
x King's Rock Quest.
x At the beach, west from PC.
x Heracross's Spawn
x North-East of Town: Position: {x = 2730, y = 4791, z = 7}.
Violet(11)
x
Position: {x = 2717, y = 4528, z = 8}.
x
Position: {x = 2701, y = 4639, z = 7}.
x
Position: {x = 2733, y = 4665, z = 7}.
x In the wild ariados >>>> {x = 2798, y = 4672, z = 7}.
x After the bridge at the begining.
x South East of Town (At Sunflura's/weep's) {x = 2733, y = 4665, z = 7}
x Next to the Gym (right)
x Hoot-Hoot Spawn (South-West from town)
x North of Black Market
x Violet gastly tower {x = 2742, y = 4539, z = 4}
x Violet >>> Girafarig spawn {x = 2821, y = 4639, z = 7}
Olivine(7)
x 2nd floor house
x Right Next to Lighthouse. (West)
x On Skarmory Spawn.
x From Skarmory Spawn to the Left.
x National Park
x Inside National Park
x West from national park
New Bark(3)
x
Position: {x = 2811, y = 4635, z = 6}.
x Ampharo's spawn
x In the umbreon outfit {x = 2763, y = 4400, z = 8}
Goldenrod(7)
x Miltank Spawn
x Stairs at Miltank Spawn
x Goldenrod Big Market
x Next to Justin Gayber
x Under the bridge
x Hard to Explain (at Position: {x = 2467, y = 4553, z = 7}.)
x At Donphans/Phanphy Spawn: Position: {x = 2641, y = 4425, z = 7}.
BlackThorn(3)
x Blackthorn graveyard
x Next cruella (Above Market)
x
Position: {x = 2946, y = 4324, z = 7}.
Ecruteak(5)
x
Position: {x = 2403, y = 4459, z = 7}.
x
Position: {x = 2688, y = 4301, z = 7}.
x
Position: {x = 2430, y = 4421, z = 7}.
x Next to the Gym
x National Park
Mahogany(2)
x From the entrance to the Left, next to a small house
x Next to Silph Corp.