In-battle glitches
If your Pokemon uses belly drum with less than half of its HP, it won't lose HP, but its physical attack will still go up 2 stages.
Love balls boost their catch rate when used on a Pokemon of the same species and gender as your Pokemon, not the opposite gender.
Dragon scales power up dragon type attacks. Unfortunately, dragon fangs do not.
If a level 1 Pokemon with medium slow leveling rate gains less than 54 experience, it will grow to level 100. However, I don't know how you can get a level 1 Pokemon.
If a Pokemon above level 100 levels up, its level will be set to 100, and it will attempt to re-learn all of its level up moves. However, I don't know how you can get a Pokemon above level 100.
If an opponent uses lock on or mind reader on you, you can still avoid certain moves by using fly or dig.
If an NPC uses a full restore while their Pokemon is asleep and has a nightmare, it will wake up but continue taking damage from nightmare. This glitch is extremely useful if you use nightmare, which you shouldn't.
In Gold and Silver and in Crystal link battles, present does a lot of damage to Pokemon whose type (second type if it has 2 of them) has a high index number.
If your Pokemon faints from sandstorm, you immediately send out 3 Pokemon that all faint from spikes, and then you send out another Pokemon that should faint from spikes, its HP will drop to 0, but it won't faint. This glitch is extremely useful against opponents that use spikes when you have 5 Pokemon with very low HP.
There are several ways to use transform to permanently change a Pokemon's species, moves, DVs, or shininess.
In-battle glitches, Crystal only
When a heavy ball is used on a wild Kadabra, Tauros, or Sunflora, its catch rate will be raised by 40.
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Other glitches
The Celebi egg glitch lets you get almost any Pokemon, a bunch of different items, and Pokerus.
If you withdraw a Pokemon from the day care, it loses experience. This is usually not useful, but it lets you EV train a Pokemon without leveling it up.
Cloning glitches can be used to clone Pokemon. I believe they can also delete Pokemon if you're not careful.
Other glitches, Gold and Silver only
You can fish and encounter Pokemon inside the Cerulean Gym.
The Trainer House glitches let you generate items.
In the Japanese version, the Bug Catching Contest glitch lets you copy data from one Pokemon to another one.
In the English version, the coin case glitches let you do a lot of different things.
Other glitches, Crystal only
If you white out from poison damage inside the Dragon Shrine before getting the TM24 dragon breath from Clair, you can get 2 TMs.
In the non-Japanese versions, you can catch Ho-Oh without needing to catch Raikou, Entei, and Suicune if you have a Raikou, Entei, and Suicune with matching ID and matching first 5 characters of the OT's name. This glitch is extremely useful if you have 2 save files and you just happen to roll the 1/65536 chance of getting the same ID on both of them.
In the German version, if you fill up your PC boxes before the Pokemon catching tutorial, you can get 999,999 money. This glitch is extremely useful if you can somehow fill up your PC boxes before the Pokemon catching tutorial.
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