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Pokémon, moves, items, anything else.

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**It's a long list...**

So yeah, I was gonna make a long list of everything unobtainable, but fortunately, I came to my senses and I'm just gonna post a link to all bulbapedia article's about the unobtainable stuff. If you think I'm just being lazy then check the revisions of this answer. It was long enough and all that was only unobtainable items from gen 1-3 and beta of only gen 1 and 2. It would have taken 3 (maybe) answers to finish and I might as well be copy/pasting the whole webpages.

http://bulbapedia.bulbagarden.net/wiki/Pokémon_Red_and_Green_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Yellow_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Gold_and_Silver_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Crystal_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Ruby_and_Sapphire_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Emerald_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_FireRed_and_LeafGreen_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Diamond_and_Pearl_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_HeartGold_and_SoulSilver_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Platinum_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Black_and_White_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Black_2_and_White_2_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_X_and_Y_beta
http://bulbapedia.bulbagarden.net/wiki/Pokémon_Omega_Ruby_and_Alpha_Sapphire_beta
http://bulbapedia.bulbagarden.net/wiki/List_of_unobtainable_items
http://bulbapedia.bulbagarden.net/wiki/Shiny_Pokémon#Unobtainable_Shiny_Pok.C3.A9mon

For the beta pages, the unobtainable stuff that is still in the code is in 'Post Release'

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"TM versions of Cut, Fly, Stength and Flash"
They were able to remove HMs all along! Curse you, Game Freak!
I have finally finished... Pokemon Red/Green Beta unused content. *sigh* Pokemon Yellow Beta and other games beta and more generations to go...
I'm uh... gonna take a break. I night's long sleep actually. It's night in my timezone right now, so I'll finish in the morning.
Aren't there always Pokemon that existed but were unobtainable? Like ?????????? in Generation 4?
Are you talking about placeholder pokemon like Missingno? They only exist because of the way data is stored. Correct me if I'm using these terms wrong, but 8-bit meant 255 bytes or pokedex entries could be stored, and 16-bit, the next step up from 8-bit, could store 65535. In the gameboy generation one and two games, there were a few empty slots that had very glitched entries that did exist but were not technically 'valid,' I guess. Invalid entries still exist in oras and I'm assuming Sun and Moon although I haven't checked it yet.

?????????? was just another placeholder would be my guess for an 'invalid' pokedex number.
Also another unobtainable pokemon is ??? type Arceus
Glitches probably shouldn't be a part of this. They aren't "coded into the game" but never made available per se -- they're the unintentional consequence of a flaw in programming. (Case in point, AZ's Floette was obviously intended at some point due to its custom model and specifications, whereas ?????????? and the like are glitches and aren't unreleased features as the question seems to request.)
?????????? had a sprite. I'm pretty sure it was added to prevent players from messing up the game by having no Pokemon.