Well, I guess I can nominate:
-Advance Wars: Days of Ruin
Not too much to say, but I do consider the "one year later" segment to be an epilogue of sorts. So, yes - Stolos is defeated, it's confirmed that Catleia's lifespan will be of average human length, the dust cloud finally clears, society can rebuild, Ed and Catleia are one screen away from entering the "kiss her you fool!" sequence, and...yeah. Good ending.
-Command & Conquer: Tiberian Twilight
Yes, really...sort of...admittedly I never finished Tiberian Twilight, but I'm more forgiving to it than most. And I do feel that the overall ending (i.e. the ending that's shared by both the GDI and Nod campaigns) is well done - caps off the series, if not the game well.
-Fire Emblem: The Sacred Stones
Not my favorite Fire Emblem game, but if judging it by its epilogue, if not ending per se, then it does rank highly. Magvel's saved, and on the way back to Renais, provided you kept the requisite party members alive, you see them set up shop back at their home kingdoms. Joshua accepts that he's to be king, Innes reaffirms Frelia's alliance with Renais, Eirika and Ephraim arrive back home to rebuild their line, we have a flashback to when Lyon met them the first time, etc. Well done.
-Golden Sun: The Lost Age
As in, past the credits, the whole group arrives back at Mt. Aleph, finding Vale destroyed, but that everyone survived. The theme that played at the very start of the duology* plays, family and friends are reunited, after all this time, the world's been saved and civilization can move forward.
*Duology in the sense that the first two games function perfectly together, whereas Dark Dawn...doesn't
-Halo 3
This is kind of iffy, but if I treat the moment from where we see John and Cortana on what remains of Forward Unto Dawn as an epilogue, then yes, it's well done. We first saw John climbing out of cryo, we last see him climbing into one, safe in the knowledge that the war's over, humanity has been saved, and the Flood neutralized. Similar to the Lost Age, this would have been the perfect place to end the trilogy. Except...
-Halo: Reach
...decided to give us a second epilogue that works just as well, if not even better. Halo 3 capped off John's story. Reach caps off the series as a whole, with Halsey's monologue and seeing life return to Reach. Halo 3 is a good trilogy conclusion, Reach is a good series conclusion. Course Halo 4 had to happen and do what Dark Dawn did (hah hah), but that aside, it's a good ending.
-The Legend of Zelda: Ocarina of Time
While not the best Zelda game or ending in my mind (if still damn good), this does have the best epilogue, if we treat the epilogue as everything that happens after Zelda sends Link into the past and he exits the Temple of Time. It's purely on the emotional level, but given the themes of OoT (time, growing up, loss of innocence, etc.), I feel the epilogue sequence conveys this excellently.
-Marathon: Infinity
Never played, admittedly, but holy shit...name one other game that ends with an AI monologuing in the final seconds of the universe before it collapses in on itself (yep, the Big Crunch Theory was correct, who knew?), pondering the final mystery of the player character.
-Super Mario 64
Shadup, the credits tune is fun and catchy, and I got my special cake. Course it counts as an epilogue. ;p
-StarCraft II: Legacy of the Void
As in, everything that goes from Raynor at Joeyray's to the end of the ending slides. I mean...wow. Caps off the game, caps off the trilogy (ending at the same place where Wings of Liberty begins, Tychus notwithstanding), caps off the whole saga. Not that Nova Covert Ops has done a Halo 4/Dark Dawn on me yet, but as I've said more than once, this was the perfect way to end the overall storyline. The galaxy is saved, much is left to the player's imagination, we can rest easy knowing that finally, peace is achieved. Not a peace that lasts long thanks to the DoM, but hey, take what I can get.
-Star Fox 64
As in, everything from where Fox defeats Andross to seeing Great Fox leaving Corneria. Nothing overly thematic or deep, but damn it, I saved the Lylat system, I got to see dear ol dad (well, if I played the hard route that is), Star Fox remains independent, fly off into sunset, see "the end" pop up. Nice touch.
-Xenoblade Chronicles
I'm kind of torn on this, as if anything, the ending is a bit too sappy, hindered by the point where a setting that's absolutely bonkers proves to me that Monolith Soft can do even larger mindscrews to the point that I feel it's to the game's detriment. Still, I'll give it a place. Whatever I feel about the ending, it's an ending that conveys the themes of the story, even if those themes are beaten over the head over and over (and Zanza won't shut up).
Yes, I actually quite like this game, just in case you're wondering.