Hold on to your hats, this is going to be a big one. I like games okay! Spoilers, also

Final Fantasy IX - Too many good ones but I would probably go now with when Brahne dies. It's a really powerful moment and shows the complexity of the relationship between Garnet and her mother. Also things really take a turn after that. Overall disc 3 is my favourite though.

Final Fantasy VIII - Attack on Garden. I dunno, I just find it exciting!

Majora's Mask - When you first rewind time and get to start exploring as human Link.

Dark Cloud 2 - The Shingala story is sweet and touching and the area is beautiful. Also a lot of outfits start opening up around then~

Tales of Symphonia - The hot/cold beverage thing. It shows that while Lloyd may originally seem to be an idiot hero, he's a lot smarter than he seems. Also shows how far along Colette is.

Suikoden V - The castle invasion near the beginning. Some gut-punches in there and it's the point where the story moves in to more serious territory.

Suikoden III - Luc's scenario. I love him and Sarah in their messed up, dysfunctional way.

Suikoden II - Predictable but the fight against Luca is epic.

Suikoden I - The ending with the emperor and Windy. It shows that Suikoden villains aren't quite so black and white.

Final Fantasy X - When you first get to the Calm Lands. So much has happened and you can just feel the weight of it all.

Final Fantasy XIII - Lake Bresha just because it is gorgeous.

Tales of Xillia - The first plot twist with the lance which really makes it stand out as not just another generic plot.

Xenosaga III - The return of Albedo because it was sweet and there was so much going on and Abel's Ark music is the best.

Fairy Fencer F - When my favourite character croaks because it was pretty heart wrenching and added some depth to the otherwise silly game.

Legend of Mana - Matilda's resolve. While I might not agree with her on everything, I appreciate her strong conviction and it was a powerful moment.

Tales of Graces f - The end of the child arc. Stuff gets srs.

Mass Effect 2 - Jacob's loyalty mission. I dunno, I just enjoyed it and the choices that came with it.

Those are the ones I can think of right now!