In no particular order.
1. Ni No Kuni/ Skull Mountain- Not so much a "gaming moment" but the whole dungeon and skull mountain sequence was just awesome to me in terms of atmosphere. Few things nail creepy, cute and cool as harmoniously for me as that dungeon.
2.Breath of Fire 2/ Finding a certain Naga Cameo Sorceress in hometown- Hidden cameo characters always get me. Being able to recruit them as playable characters makes it all the cooler.
3. Secret of Mana/ Got a few....
A. Gaia's Naval, Tropicillo and recruiting the sprite.
B. First encounter with Thanatos at Pandora.
C. Truffle King Flamie rescue.
4.Xenoblade/ Ending- Shulks dialogue coupled with the fact that you know damn well you are the brink of completing something epic culminated in "memorable" for me.
5. Earthbound/ Opening and Onet- Once again another on the list purely for atmosphere. If I had to single out a particular part it would be the arcade.
6. Final Fantasy 6/ Yep here come the predictable entries to my list....
A. Leo at Thamasa event.
B. Shadow and the Floating Continent
C. Daryl's Tomb
D. Terra's first transformation post the Narshe battle.
7. Lunar/ Ghaleon's assault on a certain dragon blew my mind when I was a little kid. I'll never forget that.
8. Tales of Vesperia/ Yuri going criminal at the end of the first act.
9. Chrono Trigger/ Zeal, Prophet events (isn't this on everyones list?)
10. Mega Man X/ Zero to the rescue
Now for a 2 that recently blew me away...
11. Tales of Xillia 2
A. The "good" ending
B. The return of
12. Lost Odyssey/ I need to give em time to sink in but....
A. End of Disc 2
B. Cecil and Rosa heading off to rescue Polom and Porom on the phantom ice train. (I got those names right didn't I???)