That golden piraka combo of Thok, Vezok, and Reidak?
And Likhan + Kikinalo
And both Toa Hagah, fully built, minus Iruini’s chest piece.
And I believe half of the first Takanuva’s vehicle. I’m honestly not sure what happened to the other halves of most of the models, and I’m missing all of their masks except the golden Thok head and Likhan’s. As for pieces, my rarest would probably be a silver Miru Nuva.
I own all good guy and bad guy sets released with the Swedish Disney comic Magazine Kalle Anka &CO those being good guy 06, bad guy 06, and bad guy 07 (the only one whose instructions haven’t gotten torn to shreds). I also own a red kaukau, a blue pakari and a blue kakama. None of these sets are particularly rare but they are the rarest I got.
I got a massive box full of Bionicle parts for £11, once. In it were all the 2005 and 2006 titans (including Kardas), Nocturn, Lesovikk, and a bunch of 2003 - 2008 figures. Most of these aren’t that rare, just expensive.