I'll try and make a list of Japanese only glitches here, I'm using Youtube as my main source because I could only understand a visual explanation, Google Translate just won't help.
Doko-Kashira door glitch: This is actually a variation of what they call 'select glitches' or item/move swap glitches, basically in the Japanese version of Pokémon Red (and Green) you could use select to swap an item with a Pokémon. This was fixed in the English version because Nintendo would acknowledge this and take that feature out. When switching items with Pokémon though its essentially like shifting variables for other bytes (because a high Pokémon 'slot' in the party will correspond to other bytes from items, to map locations and a lot more). They decided to switch Oak's Parcel with the Potion which would 'swap' the variables for a few bytes but notably make the next warp relevant to how many extra steps you take.
Surf on land: Unless I'm mistaken this only exists in the Japanese versions, a video is here http://www.youtube.com/watch?v=MhPxwdPeOwk and it involves the player using a bunny hop on a rock next to the water in such a way that he/she will be given the 'do you want to surf here' option on a normal piece of land.
Rock Smash animation glitch: Presumably if the player takes out the game cartridge when using Rock Smash the game will only freeze after the animation has finished, before that 'part of the background' will seem to move across the 'using move' screen http://www.youtube.com/watch?v=ucRpfInW8X4
Surf through Elite Four door glitch: This is probably the most well-known Japanese exclusive Pokémon glitch and involves the player surfing through Elite Four Aaron's door and into the 'void'.
Item cloning (D/P): Give a Ditto or Pokémon with Transform any hold item, and in battle make that Ditto/other Pokémon Transform into any Pokémon. If one of your Pokémon then uses Trick or Switcheroo on the Pokémon which transformed, presuming that Ditto/ the other Pokémon does not faint at the end of the battle both Ditto and the 'Tricker' will have the same items. http://www.youtube.com/watch?v=OyJg2zk6TWo
Mimic glitch: A glitch concerning a Pokémon with the move Transform and a Pokémon with the move Mimic, which after copying the move Transform can transform into another Pokémon and permanently recieve that moveset at the end of the battle. http://www.youtube.com/watch?v=OyJg2zk6TWo
Inside another player (underground): Probably not very notable, but it involves the player being 'on top' of another player if they both exit a secret base at the same time. http://www.youtube.com/watch?v=cExO3LHPVS4
Ace Trainer battle loop: Ace Trainer Deana in Route 225 - who has a level 53 Flaaffy and a level 53 Tropius if approached from three steps away will be continuously battled until the player turns the game off. The game will act as if the player was using the VS seeker. http://www.youtube.com/watch?v=OaNIKkRSYiQ&feature=related
Invisible NPC: I'm a bit sketchy about this one, but apparantly if the player decides to lead the man in Hearthome City to the contest hall one of the nearby trainers becomes invisible and can only be seen by her shadow until the man leads to player to the hall. http://www.youtube.com/watch?v=i14PJTFy9KE&feature=related