Not sure for Diamond or Pearl, though for Platinum in my initial file (which got stolen, so I got a new one), it was Fantina. She almost KOed my whole team with Mismagius. My team was Prinplup, Monferno, Grotle, Staravia, Pichu & Aipom (original, I know).
After it got stolen, I bought a new Platinum and the toughest gym was Roark. I had Piplup, Shinx & Budew. His Cranidos is so powerful and after quite a few tries, Piplup was my last one and won against his Cranidos with 2 HP left. Gardenia was also pretty hard. Took me several tries to beat her and my team was Prinplup, Luxio, Budew & Togepi.