When Banjo and Kazooie are separated in Tooie, the left behind partner will always tell the other not to leave them if they try travel too far away. Banjo will sadly ask Kazooie not to leave him alone, while Kazooie sternly declares that there's no way he's leaving without her. Goes to show that despite their arguing and snarking at each other, they genuinely do like being with each other.
Towards the end of Tooie, Jamjars swallows his pride and gives a forced apology to Kazooie in order for her to bring his dead brother Bottles back to life.
Also, in Terrydactyland, The Styracosaurus family - just the sheer amount you help a family in a dire situation (One of the children is deathly ill, another has been shrunk to a tiny size and the third is missing, trapped in a hellish amusement park) for, really, a minor reward compared to the amount of work you do - makes me feel warm and fuzzy every time. Just goes to show that you may be playing as a none-too-bright bear and a snarky bird, but they're still nice guys.
The graveside flower pots in Mad Monster Mansion. If an egg is plopped into one, flowers bloom...and a very ghostly, quavery "thank you..." intones out of nowhere.