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Combed through Pokemon. Might have missed some. Defined "late" as anything requiring Waterfall from the last gym. Mentions the Odd Egg a few times. Refers to the egg you get from the Daycare in Crystal, for the record.
Bulbasaur: Transfer only
Charmander: Transfer only
Squirtle: Transfer only
Pikachu: Route 2. (Exception: Pichu through Odd Egg.)
Clefairy: Mt. Moon (+ Route 3 and 4 in Crystal). (Exception: Cleffa through Odd Egg.)
Diglett: Diglett's Cave.
Ponyta: Route 27 (Just before the Elite Four)
Doduo: Route 27 (Just before Elite Four), although technically available via trade in Blackthorn (for a female Dragonair) in Crystal as Dodrio.
Grimer: Route 16-18 + Celadon City
Voltorb: Route 10...kinda. Obtains one via the Rocket Hideout Electrodes. Finds a trade in Olivine you can do too.
Cubone: Available in Crystal in the Goldenrod Game Corner for 800 coins. Otherwise, Rock Tunnel.
Tyrogue: Mt. Mortar gift. Requires Waterfall, which is late. (Exception: Tyrgoue through Odd Egg.)
Rhyhorn: Victory Road, although technically available via trade (for a female Dragonair) in Blackthorn as Rhydon in Gold/Silver.
Chansey: Route 13-15.
Kangaskhan: Rock Tunnel
Mr. Mime: Route 21
Electabuzz: Route 10. (Exception: Elekid from Odd Egg.)
Magmar: Appears early in Gold/Silver (Burned Tower). Delays it to Mt. Silver in Crystal. (Exception: Magby from Odd Egg.)
Porygon: Celadon Game Corner
Omanyte: Transfer only
Kabuto: Transfer only
Aerodactyl: Route 14 trade
Snorlax: Vermilion City
Articuno: Transfer only
Zapdos: Transfer only
Moltres: Transfer only
Mewtwo: Transfer only
Murkrow: Route 7 and 16. Also Route 18 in Gold/Silver.
Misdreavus: Mt. Silver
Sneasel: Not late in Crystal (Ice Path). Only in Mt. Silver and Route 28 in Gold/Silver, however.
Slugma: Route 16-18
Houndour: Route 7
Larvitar: Mt. Silver
Edit: Version exclusive list, based on the English version.
NOT in Silver: Mankey, Growlithe, Spinarak, Gligar, Teddiursa, Mantine
NOT in Gold: Vulpix, Meowth, Ledyba, Delibird, Skarmory, and Phanpy.
NOT in Crystal: Vulpix, Mankey, Mareep, Girafarig, and Remoraid.
Additional notes:
Recalls most evolution stones being in Kanto in Gold/Silver. Acquires a Sun Stone via Bug Catching Contest and a single Moon Stone via your mom. Acquires Leaf, Water, Thunder, and Fire stones in Crystal via trainer phone calls. Also grabs an extra Moon Stone in the Ruins of Alph with Surf + Flash (probably?) in Crystal, on top of the Sun and Moon stones previously mentioned.
Cannot get the Metal Coat until postgame, so no Scizor or Steelix before then either. Never mind, thanks to Megan. Finds Metal Coats with a 2% chance on wild Magnemites and Magnetons.
Edit: Added Cubone information from Rock_Salazar.
Edit2: Apparently catches Remoraid during a swarm on Route 44 with any rod. Same for Qwilfish on Route 32.
Edit3: Added the Mom Moon Stone, thanks to icycatelf.