Ohhh.... gosh. Hardest gym leader? Wow, honestly I would like to say 99.9% of them were real challenges, but my top picks are Candice, Gardenia and Volkner. Candice is honestly the only gym leader in any of the several Pokemon games I've done a complete playthrough of, that made me want to scream in frustration and smash my DS at the wall. (although that isn't very sensible, so I didn't ;___;.)
Her Froslass, with the world's most irritating move- Destiny Bond, was such a pain. With Abomasnow's ability that made it hail plus a powerful blizzard, all of my Pokemon were goners. Even with a reliable fire Pokemon alongside me, I still found it difficult to knock her Pokemon out. And then there's Abomasnow! The only thing that I was bothered about was it's irritating Grass Whistle which seemed hacked after all the times it successfully used it.
Now there's Gardenia. I have to admit, her first two Pokemon were a piece of cake. A quick Wing Attack and both of them were goners. But her last Pokemon, Roserade ;_;, was almost impossible. It used a strategy, of poisoning, using powerful moves and paralyzing. Such an evil Pokemon, even with all the attacks I could possibly used, it took ages to knock it out.
Last up is Volkner. Being the last gym leader, I'd already expected he would be a difficult opponent. But not as difficult as this. I never had an interest in ground-types so I didn't have one to help me in the fight. His Pokemon were speedy, with a diverse range of attacks and I was always paralyzed, quick attacked and caught off guard. I only managed to win, with a lucky critical hit at the end :), so if it wasn't for that I'd still be facing him to this day.
Yeah, so that's who I found particularly difficult in D/P/Pt, although I would like to say all of them except Roark are hard D:.