Not counting factory prototypes, the pre war 30-30 R has to be on the short list of rarest...
Not catalogued though, they were apparently made as special orders. If you get into special orders, there's a lot of one off specials. 99R's in 303 probably rate up there as one of the more uncommon varieties.
Obviously any non-MHG musket is way at the top of rare catalogued rifles (remember the MHG's weren't catalogued either
).
A few special grades are way up there for rarity - Monarchs, Premiers, etc. Any 1899 engraved with G style engraving.
99T's in 22HP, 99EG's in 22HP, 1899 SRC's in 38-55, 99DL's in 250-3000, 1960 99E's with schnabel tips, any 99C with double diamond checkering, cut checkered 99DL's in 284, etc..
