NES: Solstice (the hardest out of them all)
Mega Drive: Sonic The Hedgehog 2
PS1: I can't really remember. Probably Syphon Filter 2.
PS2: Most of the games I bought weren't story driven. Maybe Kingdom Hearts on the hard mode.
PS3: Ni No Kuni
PS4: I'll go with FFXIV as well doing end game stuff.
PC: Dungeon Keeper