I think my top 3 hardest was misty in FRLG, Whitney in both GS and HGSS, finnally Ghetsis.
Misty was because I was too stupid to get a grass or electric type to combat her and all I had was a fearow, a ekans, and a Charmelon.
Whitney was hard for me with only quilava at my side in GS but in HGSS i tried to use hypnosis but it woke every time (That stinkin piece of hamburger)
Ghetsis's was a cakewalk until I fought his Hydregon in BW it took out several of my members, Though using a strategy of biding my time and using revives and dragonbreath I manged to win. Ironically it only took me one try. I heard others wern't so lucky including my own brother.