Finishing up Basic D&D with its epic finale... the Rules Cyclopedia.
There are a whopping 89 monsters on the list that were core here, and never again:
- Versions of archons, undead beholders, mountain and sea giants, gremlins, phoenixes, and poltergeists unique to Basic D&D
- The gemstone dragons: amber, crystal, jade, onyx, ruby, sapphire (not to be confused with the AD&D lineage's gem dragons)
- The Dragon Rulers: Diamond, Opal, Pearl, and the Great One
- Actaeon
- Adaptor
- Blackball
- Snow ape
- Caecilia
- Elemental ruler
- Greater efreet
- Faerie
- Grab grass
- Black hag
- Headsman
- Helion
- Horde
- Hsiao
- Hydrax
- Kryst
- Malfera
- Mystic
- Mek
- Metamorph
- Mujina
- Nuckalavee
- Lava ooze
- Planar spider
- Plasm
- Revener
- Rhagodessa
- Frost salamander
- Sasquatch
- Spectral hound
- Sporacle
- Rock/cave toad
- Water termite
- Undine
- Giant bass, giant rockfish, giant sturgeon, great whale, giant snail
- Herd animals: caribou, moose, zebra
- Generic dinosaurs: aquatic, land carnivore, land herbivore, large pterosaur, small pterosaur
- Golems: amber, bone (a.k.a. skeletal), bronze, mud, obsidian, wood, drolem
- Hydrae: flying, sea
- Lycanthropes: wereseal, wereshark, devil swine
- Drakes: colddrake, mandrake, wooddrake, and elemental drake (air/earth/fire/water)
- Gargantua: carrion crawler, gargoyle, and troll
- Phantoms: apparition, shade, vision
- Spirits: druj, odic, revenant
EDIT: After the 3.0 update, remove the "great whale" from the above list - it was a renamed "sperm whale" (from the Expert Rules) and therefore counts as a generic "whale", not a variant.
Why were these included? No deep reason this time - the Rules Cyclopedia was a compilation of all four rulesets for Basic D&D (Basic, Expert, Companion, and Master) and these monsters were in those sets. A better question - which I don't have an answer to - is why Basic D&D invested so much energy in a completely different line of monsters for its game, rather than just cribbing from the AD&D monster books.
The other question is, why has the main D&D line (AD&D onward) been so reluctant to include these Basic monsters in later core lineups? 3e tried, with the athach and nightshades, but that's pretty much been it. It's even rare to find these monsters updated in non-core books for later editions (excepting the Mystara MC in 2e, which pretty much had "update Basic D&D monsters" as its remit).
Worth noting, BTW - although not Wizards-official, the Original Adventures Reincarnated line did update a number of these monsters for 5e. (Shame those products will probably never see a PDF release.)
EDIT:
@Joshua Randall noted that grab grass is in 4e; to be more specific, it's in the DMG as a trap. That still means it's not a core monster (since not in the 4e MM or MV), but figured I should note it here!