If we're talking individual Pokémon, definitely the super-rare Safari Zone Pokémon from Gen I: Scyther, Pinsir, and Dratini to some extent, but Tauros, Kangaskhan, and of course Chansey were the worst. And even if you encountered one, there was a very good chance that they would run away. >_<
But even those are simple when compared to Hidden Ability hunting. I started doing it about a year ago now, and I still have about thirty left to find. Of these the hardest are Qwilfish, Basculin, and Hippopotas, which, in addition to a number of others like Sentret which I did manage to get my hands on, can only have their abilities if they or a parent was transferred from Gen V(and they can only get these abilities in those games via a method that no longer exists). This likely won't be a problem for Qwilfish much longer though thanks to the Gold and Silver coming to the Virtual Console later this year.
And of course there's Regenerator Mareanie. Anyone who's looked for one knows what I'm talking about. *shudders*