Off the top of my head,
RBY/ FRLG: Chansey (except in Red and Blue), Tauros, kangaskhan, Legendary Beasts in FRLG that are nearly impossible to find and can glitch when they roar
GSC: Yamna, Snubbull, Dunspare, and I think remoraid.
RSE: Feebas, Latias and Latios, Gen 2 starters (not catch but annoying to obtain)
DPPt: Feebas, Munchlax, Spiritomb
HGSS: Beldum in the safari zone
BW/BW2: none that I can remember
XY: None
ORAS:None, Pokenav makes it too easy
SM: Beldum in the wild, Castform, and Politoad
USUM: Beldum, Castform, Larvesta, and Golett/Baltoy (Rare SOS encounters in the desert that can selfdestruct)
