When Wes and Rui break into Plusle's cell, the little guy looked really happy to see you. Personally I thought that was heartwarming.
Seeing Celebi appear after using a Time Flute.
Receiving Jirachi from the Pokemon Colosseum Bonus Disc. What a Tinker Bell imitator! I got to admit 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!
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?)