Amy showing that she's serious about her love for Sonic. "If I had to choose between the world and Sonic, I would choose SONIC!"
Elise's line is similar - the difference being that by now everybody knows the world's about to go to hell in a handbasket if she does play it that way. And because it's Elise; there's a whole plethora of things wrong with being Elise.
Sonic and Elise's reunion, just before he fights the Egg Wyvern.
When Elise revives Sonic.
... which is followed by a heartfelt thanks from Sonic.
Something of note in the Japanese version: throughout the game, Sonic usually says "Thanks" in English. He doesn't here.
The final cutscene, After Elise blows the flame out, supposedly guaranteeing that they would never have met and won't have any memory of each other whatsoever, then Sonic arrives to the festival we see at the beginning of the game, when he causes a wind to go past Elise, she shows a sign that she might still remember Sonic after all.
...which is followed by a shot of Sonic smiling down at Elise from afar, giving us the freedom to believe that Sonic remembers Elise too.
The beach scene with Team Dark. Really shows how tight knit a group they are.
The moment where Amy rescues Sonic from being killed by Silver and more importantly Sonic expresses his gratitude for her.
Shadow is also the second character to save Sonic from being killed by Silver. This proves he does have mutual respect for his blue rival.
Despite the infamous kiss scene, there's the revival of Sonic, and all of the characters show relief that the main hero is alive and well.
Near the end, when Pokecapn really cannot withstand this game anymore, the other goons take over until he decides that he can, assigning themselves characters. Pretty much summed up with KFJ's exclamation of "Aah, teamwork!"
When the game is finally over, the four remaining members of the group read through the end credits in order to find out whose "fault" the game was. Many vocal critics of the game tend to be irrational when talking about it, bashing every little aspect and calling for the heads of everyone working at Sonic Team or Sega in general, but the gang makes an honest effort to discern between those who should and shouldn't be blamed for the poor quality of the game, and they even pity the team members who had to make tough decisions and deal with pressure from those who were truly at fault during production. It also showed that the "healing" had already begun; despite all the angry shouting and apparent Sanity Slippage during their playtime, the crew were all still friends and able to make rational judgements without lashing out, which is more than you can say for most internet Sonic fans.
So we can basically say that about 80% of the staff on this game are good people, and they did good work.