First, I'd like to second a few things that people have already mentioned:
Restoring a Guardian Sapling in Okami. Watching the entire area just flood with life is truly a gorgeous sight to behold.
The final blow against a difficult boss in pretty much any game ever. Seeing that sucker FINALLY go down after trying again and again and again to beat him, her, it, or them...ahhhh.
Pretty much the entire world of Shadow of the Colossus. One of my favorite things to do in that game is find a nice, high clifftop with a stunning view of the surrounding panorama...spend a good few minutes taking it in...and then jump off.
And now, some stuff that hasn't been mentioned yet:
The dragon ride after escaping from the Draracle's Museum in Lands of Lore II: Guardians of Destiny.
The cutscene in Legacy of Kain: Blood Omen where Kain beheads Moebius. Especially if you've played the other games in the series and know what a tremendous bastard Moebius is. I literally cheered...and then reloaded from a save just to watch it a few more times.
Similarly, the cutscene in Legacy of Kain: Defiance where Moebius gets skewered by Kain...and then again immediately afterwards in the Spectral Realm by Raziel. And then AGAIN when Raziel reanimates his corpse! HAH. TAKE THAT.
Also, I love swimming in World of Warcraft, especially in areas close to the shore where you can see all the underwater scenery--plant life, sunken debris, fish, etc. It's so peaceful. The very first time I played, I started off as a Draenei Warrior, and I swam around the entire perimeter of Azuremyst Isle just enjoying the sights.