When Andrew first looks in the mirror to see his new human features, he gazes deeply in the mirror, as complex emotions play on his face for a long while. He finally quietly tells Rupert, "Thank you" in the most understated way.
Blink and you'll miss it, but when Andrew adopts the dog late in the movie, he names it Wolfie, the same name Little Miss named her stuffed-toy dog way back near the beginning of the movie.
On Little Miss' death bed, she still has the little wooden horse Andrew made for her, which was his first sign of individuality.
The Together in Death ending, of course, is both this and a Tear Jerker. The implication that the nurse is Galatea and has also gained individuality makes it more heartwarming.