FFIV Advance: Kain's post game trial.
Etrian Odyssey: The boss fight against Fenrir. I was unaware at the time that F.O.E.s could enter regular battles or even boss battles. It made for a great fight when a Skoll entered the fight every now and then.
FFVIII: Triple Triad had me pretty addicted.
BoFIV: The scene at the top of the windmill or when the party just consists of Ershin.
the final boss convinced me to join him. One or two of his points were flawed but overall "Maybe so" was answeredSMT Devil survivor: There was something about that one good police officer that I loved. Whether it was the fact he was willing to take on demons without a COMP or that he was the only one not clapping when the Shomonkai rescued them.
I went through most of the game wondering why none of the rune of punishment bearers just chopped off their hand and when you find out Cray did just that it was pretty awesome, for me at least.
Phoenix Wright Justice for all: The final trial concerning the Nickel Samurai.
You have to choose whether Adrian Andrews is found Guilty or Maya gets killed. Your choice turns out to be irrelevant but at the time I just stopped playing for five minutes to think it over. In the end I chose to sacrifice Maya for the greater good.
Dislike:The "prologue" of Suikoden V. I really enjoyed it my first playthrough but I was wishing for it to end quickly on my second. Now I have a seperate save just when you arrive at Barrows.
BoF Dragon Quarter: The part where you realize there is no way to lower the D counter. Hope you were not spamming it. (I actually really liked this game overall even if it took some adjusting to)
FFX: The butterfly minigame. This really got on my nerves.
Xenogears: That rock paper scissors game drove me insane. Technically it was optional but I always felt obliged to complete it.
Suikoden Tierkreis: Realizing that collecting 108 stars of destiny affected almost nothing in the game.