FFIV - Everything between getting Edge and obtaining the Lunar Whale, this section just kind of drags on and I could have doen without the second trip through the Babel Tower

FFVI - Mt. Hobbs and getting Sabin, it just feels out of place for me.

FFIX - Everything after the fight between Alexandria and Bahamut

FFXII - Getting to Archades, probably the longest stretch of the game without anything significant happening.

Xenogears - Either Babel Tower or Rico's Anima Relic Dungeon.

Xenosaga Episode 1 - The whole section between the Shion and Ziggy's group finally meeting up up until the Cathedral Ship section. A bit boring.

Suikoden - Neclord

Suikoden II - Either Greenhill or Neclord again.

Suikoden III - Chapter 4, smurf chapter 4.

Suikoden IV - The deserted island section after being exiled.

Suikoden V - The Dragon Calvary section.

Breath of Fire II - Getting Spar, long ass side quest.

Breath of Fire III - Making the Shizu dinner for the mayor. Pain to gather all the ingredients, even more of a pain to make it right.

Breath of Fire IV - The entire section between Ryu and co. getting back to Wyndia and Cray being put on trial all the way to heading north to get a boat. Also, Fou Lu's Tomb.

Breath of Fire V - The battle against the 3 special Rangers, doing the optional dungeon is a pain in the ass as well.

Wild Arms 2 - Anything that involves Tim being the focus.

Chrono Trigger - The first Prehistoric time section. Its a bit too scripted, the dungeons are annoying and a completionist nightmare and the section drags on longer than is necessary.

Chrono Cross - Doing the Marbule quest since it's easy to screw up. Fort Dragonia is also a pain in the ass despite the story pay-off at the end of it.

SMTIII Nocturne - Matador if you're unprepared for him, the Ginza Underpass is probably one of the more tedious sections of the game, especially if you plan on fighting the optional Oni.

Persona 3 - May through July, not going to lie, it's not exactly the most riveting section of the story.

Persona 4 - The Last day when doing the true ending. It just always felt a bit tacked on to me and the real villain wasn't as interesting or compelling as the actual Serial Killer and final boss of the normal ending.

MG2 - The Keycard trick

MGS1 - The Keycard trick redux

MGS2 - Emma, smurf Emma Emmerich

MGSV - Any mission that involves the Parasite Soldiers.

MM2 - Wily Stage 2

MMX - Any stage that involves rail fighting. (moterbikes, the hover craft etc...)

Legend of Zelda - Sixth and seventh dungeons

Link to the Past - Turtle Rock

Link's Awakening - Turtle Rock and Face

Ocarina of Time - Fire Temple and all the crap you have to do to get to the Shadow Temple

Wind Waker - The entire search for the Triforce Shards

Twilight Princess - Water Temple

Skyward Sword - Learning how to use the parachute, and trying to reach the Water Temple.

Vagrant Story - Snowfield Forest

Brave Fencer Musashi - Steamwood, smurf steamwood...

Dragon Quest VII - Dharma Temple

Arc the Lad 2 - The final stretch of the game.

Armored Core 2 - Any mission involving fighting off the native martians.

Kingdom Hearts - Atlantica and Monstro

Kingdom Hearts 2 - Pirates of the Caribbean and doing the second round of each world.

Robotech BattleCry - Escort missions

I'll think of more as time goes by.