Yes, there are quite a few.
(I will be including Pokemon that you can encounter when walking in a puddle.)
R/B/Y:
Dratini when fishing in the Safari Zone
Dragonair when fishing in the Safari Zone (Yellow only)
G/S/C:
Grimer and Muk when surfing in Celadon City
Dratini when fishing on Route 45 and Dragon's Den
Dratini when surfing in Dragon's Den
Dragonair when fishing on Route 45 and Dragon's Den
R/S/E:
Zubat and Golbat when surfing at Seafloor Cavern, Meteor Falls, and Shoal Cave
Solrock when surfing at Meteor Falls (Ruby and Emerald only)
Lunatone when surfing at Meteor Falls (Sapphire only)
FR/LG:
Koffing when surfing in Celadon City
Grimer when fishing in Celadon City
Dratini and Dragonair while fishing in the Safari Zone
Hoppip when surfing in Water Labyrinth, Five Island (Town), Resort Goreous, Five Isle Meadow, and Memorial Pillar
D/P/Pt:
Zubat when surfing in Mt. Coronet, Oregurgh Gate, and Ravaged Path
Golbat when surfing in Mt. Coronet, Oregurgh Gate, Ravaged Path, and Victory Road
Masquerain when surfing on Route 229 (Platinum only)
Dratini and Dragonair when fishing in Mt. Coronet
HG/SS:
Grimer and Muk when surfing in Celadon City and the Safari Zone
Dratini when surfing in Dragon's Den
Dratini when fishing in Dragon's Den and the Safari Zone
Dragonair when fishing in the Safari Zone and Dragon's Den
Duskull when surfing in the Safari Zone
Jumpluff and Skiploom when surfing the Safari Zone
Masquerain when surfing in the Safari Zone
Murkrow when surfing in the Safari Zone
B/W:
Shelmet when walking in a puddle in Icirrus City, Moor of Icirrus and Route 8
Stunfisk when walking in a puddle in Icirrus City, Moor of Icirrus and Route 8
Stunfisk when surfing in Icirrus City, Moor of Icirrus and Route 8
Stunfisk when fishing in Icirrus City, Moor of Icirrus and Route 8
Dratini, Dragonair, and Dragonite when fishing outside of Dragonspiral Tower
Croagunk when walking in a puddle when a swarm is happening on Route 8
B2/W2:
Croagunk when walking in a puddle in Icirrus City, Moor of Icirrus and Route 8
Karrablast when walking in a puddle in Icirrus City, Moor of Icirrus and Route 8
Shelmet when walking in a puddle in Icirrus City, Moor of Icirrus and Route 8
Stunfisk when walking in a puddle in Icirrus City, Moor of Icirrus and Route8
Stunfisk when surfing in Icirrus City, Moor of Icirrus and Route 8
Stunfisk when fishing in Icirrus City, Moor of Icirrus and Route 8
Dratini, Dragonair, and Dragonite when fishing outside of Dragonspiral Tower
Azurill when surfing at Floccesy Ranch and Route 20
Grimer and Muk when surfing in Castelia Sewers
Grimer and Muk when fishing in Castelia Sewers
X/Y:
Dragalge when fishing in Cyllage City, Ambrette Town, and Route 8
Masquerain when surfing on Route 3
Goomy when surfing on Route 14
Sliggoo when surfing on Route 19
Stunfisk when surfing on Routes 14 and 19
Dratini and Dragonair when surfing on Route 21
OR/AS:
Zubat when surfing in Scorched Slab, Sealed Chamber, and Meteor Falls
Golbat when surfing in Scorched Slab, Seafloor Cavern, Sealed Chamber, Meteor Falls, and Shoal Cave
Solrock when surfing in Meteor Falls (OR only)
Lunatone when surfing in Meteor Falls (AS only)
Masquerain when surfing on Routes 102, 111, 114, 117, 120, 123 and Petalburg City
TL;DR:
Zubat and Golbat are everywhere and you have no place to hide.
Sources: This, this, this, this, this, and this. (I looked at every City, Route, Cave, etc. listed there.)
