Metal Gear Solid 3 and MGS4: Guns of the Patriots.
With MGS3, it was the room full of people celebrating Jack, followed by him visiting the grave site of The Boss...fantastic stuff. This is an example of when Kojima does it right, it's not convoluted or overtly long, it was absolutely appropriate.
With MGS4 it was the end of an era, Snake (and his story) finally comes full circle. It was a bit long, but again appropriate giving that Snake's legacy isn't the easiest to wrap up, you've got to close up a story arc that takes 40 to 50 years, so I didn't ***** like a lot of people.
After it's completely over, I always imagine Snake going back to Alaska mushing dogs, hanging out and havin some drinks with Otacon, or maybe finding some Inuit girl. Just living a peaceful life with the time he has left.