When Wes and Rui break into Plusle's cell, the little guy looked really happy to see you/Wes.
Once returned to Duking, Plusle asks to go with Wes and Rui. That's right, this little guy was not given to Wes as a gift, nope. Plusle "wanted" to join them in their fight against Cipher!
Seeing Celebi appear after using a Time Flute.
Receiving Jirachi from the Pokemon Colosseum Bonus Disc (what a Tinker Bell imitator). Must admit it though, the way it blinks at you is just so cute.
Wes has an Espeon and Umbreon, two Pokemon who can only be obtained via friendship. Even when he was a villain he was nice to his Pokemon! Awww!
In each Pokemon's profile is a log of where you caught that Pokemon. Espeon and Umbreon's? "Players old friend."
Not gonna lie, any time a Shadow Pokemon gets rehabilitated and reopens the door to their heart gives me the warm fuzzies. That triumphant fanfare really adds to the moment.
I found it really sweet that Rui still decided to trust Wes even after finding out he was a former member of Snagem. She only recently just met the guy but she's going to stick by him, and I found that incredibly thoughtful on her part to look past his background like that and just trust him, like a true friend. (or is she?)
The backstories behind Eevee and Togepi. Awww!
If you beat Greevil again after purifying all Shadow Pokemon, you'll see a brief cutscene of the hero putting his Snag Machine away, as it's not needed anymore. Gives a nice feeling of closure.