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As far as event legendaries go, it'd have to be Meloetta and Genesect that are the rarest.
>Mew has had several distributions during gen IV, as well as technically catchable in-game in gen III
>Celebi used to be the rarest, but then gen IV gave it out for HGSS and bank gave it out for free
>Jirachi is rare in the west, but colosseum bonus disc is usable anytime and Japan gets a Jirachi distribution literally every year
>Deoxys was distributed loads of times as well as being catchable in gen III via item and gen VI via ORAS
>Manaphy eggs were given with basically every Ranger game as well as distributed once or twice via in store event
>Darkrai and Shaymin are both easily catchable in gen IV via glitch/item, as well as both having multiple WC distributions
>Arceus was catchable in gen IV, although the item to access it was never distributed. Also had one event distribution and a Dreamworld distribution
>Keldeo has its distribution twice during gen V, as well as the recent distribution via that stupid point system or whatever in Japan
>Meloetta was distributed twice, but only in gen V
>Genesect was only distributed in gen V
>Victini was only distributed in gen V, but the Liberty ticket can easily be hacked in to catch in-game
>Hoopa and Volcanion are unreleased
>Diancie codes are still redeemable and easily obtainable at this time
The rarest of the rare will always be SPACE C Deoxys and other semi-obscure gen III events, though.