Here are some I can think of for me:
FFIX - Fossil Roo and Ipsen's Castle. Neither excited me.
FFX - Mandatory Blitzball. Ugh the dread each time. EACH TIME.
FFVIII - Rescuing Rinoa... IN SPACE~~~
Majora's Mask - Stone Temple Tower. Too complicated for my puny puzzle solving mind.
Trails of Cold Steel - Nord Highlands. Beautiful but just too big and drags on forever.
Star Ocean IV - Cardawhatever Mothership. I HATE that section with a passion. So unbelievably annoying.
Tales of Symphonia - Long ass sewer puzzle nonsense.
Dark Cloud 2 - Heim Rada and Mount Gundor. So ugly and uninteresting.
Dark Cloud - First dungeon not because it's bad but just because it's hard.
FFX-2 - Chapter 4. Everything is just through the CommSphere and I don't.... eh
Fire Emblem: Awakening - Getting Severa. SO HARD.
Bravely Default - The repeat parts.
Xenoblade - FRIGGIN XORD.
Xenosaga - Anything involving mechs.
Xenogears - MECCCCHHHHHSSSSS
Persona 3 Portable - Towards the end of Tartarus.
Threads of Fate - The platforming sections when you go visit Fancy Mel
Kingdom Hearts II - Prologue
Those are the ones I can think of for right now.