In Sapphire, mine was probably Fortree's gym. The puzzles really annoyed me, but were fun - I hate how they're easier in Emerald. And Altaria was incredibly difficult to beat. Dragon type (loads of resistances) + Earthquake (loads of things weak to it) = pain.
That was in the days when I was a noob. Good old days.
I miss those good old noobie days... *sighs*
Anyway, I agree, Fortree Gym's Altaria was an absolute
pain! I mainly relied on my Blaziken, and all my other Pokemon couldn't really stand up to Earthquake or they were terrible agaist the Dragon-type. And to a lesser extent, Swellow with Aerial Ace crippled my Blaziken. Sheesh...no love for a fellow bird!
Brawly was also difficult, if he Bulk Up-spammed and followed with a Fighting move, that was really hard to recover from. Especially when his darn Makuhita did that! Peck, Focus Energy, and Double Kick were lifesavers, but it was hard not having STAB for Peck...
Wallace
should have been hard for me, but oddly enough, I won with ease when I had Sapphire, despite using Kyogre against Water-types and having Blaziken as my starter...
Flannery was difficult with her Attract+Sunny Day+Overheat combo, and her occasional Rock Throw was annoying.
Everyone else was pretty easy...I loved defeating Norman with Fighting moves. But when I played through with Mudkip or Treecko, I could never get past him! But I think I was
really lazy when training those starters, unlike Blaziken.. :D
So IMO, Brawly, Flannery, Norman (w/out Torchic), and Winona were the most difficult Gym Leaders to beat.