At the end of the main storyline, N jumps out the hole in the wall of the top of his castle. Instant cut to the best end credit music you'll ever hear, with the 3D model of the version legendary people playing the other version will see at the title screen. Later into the credits, you see N riding that Pokémon across the skies.
If you've played MOTHER 3, the music just makes that cutscene even better. The song, N's Farewell, takes notes from that game's Love Theme, which is played during its most heartwrenching moments - and considering what MOTHER 3is known for...
When N first encounters the legendary dragon at the top of Dragonspiral Tower. Or the moment when Reshiram/Zekrom is summoned in N's Castle, and it comes crashing through the walls.
And after that as well when the player's dragon gets summoned, saving the player from N and his dragon, with the awesome music at the same time.
Add to it the fact that if you made it to N with a free space in your party, the moment you catch your dragon, it will be added at the top of your party, meaning that the first fight will be between Reshiram and Zekrom
You don't need the free space. If you have a full party, you'll be asked if you want to swap the dragon into your team for the duel with N. Game Freak knows that's all you want, heck yeah, bring it on!
It's even better because those Com Mons have quite possibly been with you since the beginning of your journey. You don't need the legendary dragon, you have your Pokemon friends! And what better way to prove to N once and for all that his idea to separate Pokemon and People is wrong than by you and your Pokemon working together to bring his Olympus Mon to its knees?
Going across the Skyarrow Bridge for the first time. It WILL bring you to tears, especially if you're a long-time fan. The World Is Just Awesome doesn't begin to describe it.
Themusic that plays on Skyarrow Bridge definitely adds to its awesomeness.
It gets even better because on the other side of that bridge is Castelia City. The biggest and most complex city in Pokémon history as of then with music as awesome as the architecture.
Whenever you've fought the Gym Leader down to his/her last Pokémon, and an awesome remix of the main theme starts up. It will make you want to kick butt that much more.
You've finally earned all eight badges and now head to the Victory Road where at it's peak is the Pokémon League. But before that, you need to pass through gates locked by badges you've earned on your journey to be the champion. Not only that, the music slowly builds as you go through each checkpoint! You're almost there, don't give up!
And it only starts when you've passed the first gate - when you first enter the area, it is in complete silence. It feels almost mystical. Kind of like Mount Silver in HGSS or Mt. Coronet in DPPt.
One of the most awesome things in this part? what the NPC says after you show them the badges, gave me a lot of goosebumps
Trio Badge Check Gate: "Oh, holder of the Trio Badge! Challenge all that you face!".
Basic Badge Check Gate: "Oh, holder of the Basic Badge! Show the knowledge you've obtained!".
Insect Badge Check Gate: "Oh, holder of the Insect Badge! Fight valiantly like an insect!".
Bolt Badge Check Gate: "Oh, holder of the Bolt Badge! Unfurl a shocking battle!".
Quake Badge Check Gate: "Oh, holder of the Quake Badge! Make your foes' hearts tremble!".
Jet Badge Check Gate: "Oh, holder of the Jet Badge! Blast ahead with tremendous force!".
Freeze Badge Check Gate: "Oh, holder of the Freeze Badge! Show the sharp edge of an icicle!".
Legend Badge Check Gate: "Pass through Victory Road, which lies beyond here, and head for the Pokémon League! Prove that you, too, can be a legend!".
Climbing up the rooms to each member of the E4. The entire endgame is just a series of CMOA, really.
When you get to N after beating the Elite Four and your Stone finally responds to you, the following cutscene is pretty neat. The Stone rises into the air, starts pulsing with energy and then turns into a curled-up dragon. And then its eyes open, and you know stuff is about to get real.
Even better, this is just after the cutscene of N calling forth his dragon, who bursts through the wall behind the throne (the hole this makes being the one they exit through at the end) and releases a massive burst of energy which vaporizes the water at the bottom of the room. When the player's stone reacts, the game says it's "absorbing the atmosphere" which suggests that, even asleep, your dragon recognizes its opposite number and wakes up specifically to kick some ass.
An awesome moment stemming from one of the harshest Tear Jerker moments in the series: Ghetsis finally shows histrue colors, sends N into broken silence, and prepares to fight the player character. And then you go and you beat the everloving heck out of him and his for messing with your new friends. And it is one of the most badass fights in the game, and one of the most satisfying Pokémon battles in the entire series.
Brycen spotting hidden Shadow Triad outside his Gym like it was nothing. Mind you, they're more or less ninjas, so spotting them isn't easy.
And then he goes and helps you and Cheren against Team Plasma, despite the fact that this is immediately after your gym battle (and he and his team would logically need a break after that). The gym leaders are just awesome in this game.
More gameplay based, but for the first time in the series you can encounter a Psuedo Legendary, Dragonite, out in the wild and actually capture it.