Secret of Mana - Probably the Empire.
Legend of Mana - Jumi Arc, pain in the ass to do, but easily the best of the three main arcs.

Chrono Trigger - Kingdom of Zeal, easily one of my favorite locations in a game.
Chrono Cross - Dead Sea, probably the biggest twist area in the game and one of the most challenging bosses in the game.

SaGa 1/Final Fantasy Legend - Suzaku's world of a destroyed Tokyo.
Romancing SaGa - Silver's treasure was kind of a nice adventure.
Romancing SaGa II - Either the mermaid quest, or the events surrounding Rocbouquet and the Amazons
SaGa Frontier II - Gustave's Chapters or Rich's Chapters.

Xenogears - Shevat and Solaris
Xenosaga Episode 1 - Cathedral Ship and the story of Cherenkov
Xenosaga Episode 2 - Return to Old Miltia
Xenosaga Episode 3 - Either the entire flashback arc, or the battle against Yuriev in Abel's Arc.
Xenoblade Chronicles - Eryth Sea since I feel like that's when the plot really starts.

The Last Story - The Haunted Mansion
Vagrant Story - The Final Area
Front Mission 3 - Emma Route: Return to Japan

Suikoden 1: Taking Moravia
Suikoden II: Pretty much everything after Luca Blight's death.
Suikoden III: Chris' first two chapter, all three of Geddoe's chapters, and all of Thomas' chapters
Suikoden IV: Taking back Razril
Suikoden V: The entire prologue leading up to the Prince fleeing the capital.
Suikoden Tactics: Entering Kooluk

Lufia 2: Hunting down Gades

Shin Megami Tensei: Ginza arc where you meet Alice and a terrible running gag begins.
Shin Megami Tensei III: Either the Obelisk or Diet Building
Persona 1 - SEBEC Arc: Alaya Cavern/ Snow Queen Quest: Nemesis Tower
Persona 2 - Innocent Sin: Caracol/ Eternal Punishment: Sanitarium
Persona 3 - October through December
Persona 4 - Heaven
Persona 5 - The last two "official Palaces"
Digital Devil Saga Part 1 - The "Totally Not Disney Land" park

Breath of Fire 1 - The Time Key quest
Breath of Fire II - Jean's Recruitment of the return to Gate
Breath of Fire III - The Outer Continent
Breath of Fire IV - Fou Lu's sections
Breath of Fire V - The Regent's sector

Metal Gear - The last building
Metal Gear 2 - The last stretch where you face Grey Fox and Big Boss
Metal Gear Solid - Tough one...probably the section between escaping the torture chamber and ending with the Raven battle.
Metal Gear Solid 2 - Tanker mission
Metal Gear Solid 3 - The battle with The End up until you reach Grozny Grad
Metal Gear Solid 4 - Probably the third act
Metal Gear Solid V - The entire Africa Arc
Metal Gear Solid: Portable OPS - Rescuing Big Boss

Devil May Cry - Probably the ghost ship section
Devil May Cry 3 - Going to the demon world