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A small thing, but Balin's friendship with Bilbo. He's the only one who would go with Bilbo part of the way into Smaug's lair and even carried him back out. In the epilogue, Balin visits Bilbo in Bag End and they happily reminisce over the old times together.
In the books, Dori was always the one who carried Bilbo and made sure he was safe, even climbing down a tree when the wargs attacked to boost Bilbo up to safety!
This line in the last chapter.
... and though many shook their heads and touched their foreheads and said "Poor old Baggins!" and though few believed any of his tales, he remained very happy to the end of his days, and those were extraordinarily long.
Although it's not quite as explicit as in the movie, Thorin's friendship and later reconciliation with Bilbo even though that was a Tear Jerker due it being on Thorin's deathbed were quite touching considering howdifferent the two were. Particularly nice is when Bilbo is complaining about how dreary Erebor is and Thorin laughs and tells him to wait until it's been cleaned and redecorated, implicitly inviting Bilbo to stay or return at some point to see Thorin's kingdom restored to glory.
Hey, what about the Elvenking's response to Bilbo giving up the Arkenstone to attempt to keep things civil? He's the first to ask Bilbo not to return to the Dwarves, explicitly because he was worried that Thorin wouldn't react well when he found out what Bilbo had done (and as it turns out, the Elvenking was right to worry). I know he isn't the nicest, most altruistic character in the book, but I found the scene downright redeeming for the Elvenking!
The Elvenking ignores a dragon hoard he believes to be unguarded, to provide relief aid after the wreck of Laketown. He doesn't even just send the baggage train - he diverts his entire army to help. One of the most altruistic acts in the Tolkien canon, and very few readers seem to even notice it.
He's also the only one who hesitates to openly go to war over the gold of Erebor. "Long may I tarry, ere I begin a war for gold," are his exact words.