I'll go a little bit off script with my answers because honestly I don't remember the names of most of the missions, I just remember the feeling that they've given me after playing them. Some of my other favorites have been listed so I'm not going to relist them as I will do the following.
When the GOAT assassin meets the Legend, plus the discussion of Desmond. The 3 most important characters in the Assassin's Creed franchise in one setting. Many franchises wish they could have a moment as significant as this on their series.
Sonic is fun when unshackled, breezing through a level. I'm not going to lie and say I've played all Sonic games but the good ones, I have. Rooftop Run is some of the most fun I've had in a game. It encapsulates all that is great about Sonic, distilled in a near perfect package. Music, colorful, expansive, control, etc. In Unleashed or Generations (I prefer the music in Generations more) To me, the GOAT Sonic level.
Discovering Hyrule Castle in the Wind Waker. This is when Nintendo started to finally listen to the fans and at least pretend to give a shyt about the timeline. Seeing the Link from Ocarina of Time immortalized like that was a big
for me.
Another Zelda moment is Snowpeak Ruins from the Twilight Princess. This isn't your typical Zelda dungeon. It has a story on top of the main story and what is going on here is rather unconventional for a Zelda game. There are the usual Zelda tropes but some things going on here probably propelled Nintendo to make Breath of the Wild in this manner, meaning not a lot of hand holding, big, etc. Just an awesome dungeon in a Zelda game that is very un-Zelda like.