I can't really decide on my rarest item, so heres all the items/mounts and such that I think are rare.
Vanilla
Rhok'delar, Lok'delar, Ancient Sinew Wrapped Lamina (which is now a 24 slot bag :P), original Grunt title (sadly just Grunt), Spectral Essence from Scholo, Argent Dawn Commission, Seal of Ascension (Key to UBRS), Onyxia Tooth Pendant and an extra Head of Onyxia from 60 Ony and Heart of Hakkar, Carrot on a Stick and Luffa :P
TBC/WotLK
Hand of A'dal, Tiny Voodoo Mask from ZA, Haunted Memento + Argent Tome + Monster Slayer Kit + Argent War Horn, Vampiric Batling AND Arcanite Ripper all from Pre-Wotlk Event
Cata
Pureblood Fire hawk, Life-binder's Handmaiden, 4.2/4.3 Meta Mounts when they were current -- I don't know how rare you would call those