The moment where Amy rescues Sonic from being killed by Silver and more importantly Sonic expresses his gratitude for her.
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.
Shadow is also the second character to save Sonic from being killed by Silver followed with Shadow glancing back to make sure Sonic's ok, and for Sonic giving him a thumbs up in gratitude before leaving after Eggman. It shows the mutual respect the two rivals have for one other.
And looking at this, just makes the scene all the more heartfelt. Even the title of the artwork warms you inside.
There's also the scene where Sonic shows no hard feelings for Silver for trying to kill him in their previous meetings, although this is after Silver explained that there was a misunderstanding. This also counts as one of the instances where Sonic shows forgiveness to a former enemy/rival.
The beach scene with Team Dark. Really shows how tight knit a group they are. This exchange in particular, after Shadow learnt that Omega would eventually be forced to imprison him in the future, due to Iblis being released, must count for something, no matter if you see this as a Ship Tease or Friendship Moment.
Rouge: Even if you believe that the whole world will be against you... know that I'll always remain by your side. Remember that. Shadow: ...I will.
This turns into a Tear Jerker when you really think about it. Shadow is immortal and will never die of an illness either, Omega's a robot which means he can't pass away either. Rouge however, is neither of those things, and will die from either old age or illness. There's a decent chance that after Rouge passes away, no one will be by Shadow's side and he will be caught fairly easily.
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.
There's also all of the characters (Eggman and Shadow included) expressing relief that Sonic is alive and well.
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 Trial Of Love. You are given a choice between Amy and Elise, and should you choose Amy, the guy who gives you the trial will say, "So, I see you have chosen your long time love. " Aww, They Really Do Love Each Other.
Maybe it's just me, but listen to these quotes from the final boss battle:
Sonic: (To Silver) Do you still have ring energy? Use the Y/Triangle Button to switch with me. Silver: (To Shadow) Hey, you're running short on rings! Use the Y/Triangle Button to switch with me. Shadow: (To Sonic) Are you ok? Use the Y/Triangle Button to switch with me.
While Sonic/Silver are concerned that Silver/Shadow are running low on rings, Shadow is concerned if Sonic's ok. That's quite a lot coming from someone who considers Sonic to be his arch rival.
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.
Alternative Title(s):Sonic The Hedge Hog 2006 Lets Play