Most rare item in game. (opinion)

[KingFu]

L1 Fine Gold Plating (Epic) [Used for crafting the Crown of Persistance]
L1 Ruby Gem (Rare) [Used for crafting the Crown of Persistance]

There are still several active in game. Certainly rare, but not the rarest.

As Doll said, there are multiple items that there's only a single active version of. There are also a few that are very likely "extinct," much of which coming from original plat store character bundles. My pick would be level 25 Ruby Gem Blade of Legend. I'm pretty sure it was discontinued during 25 cap when some of the FC items were added. Only one I have ever seen was owned by a collector who quit at level 35 cap.