In the Final Mix version of the end to the second visit to Twilight Town in the first story, Sora's reunion with Kairi. It's less the actual reunion than it is the fact that Alex knows that they all are aware, in spite of the fact that Alex was only doing it for himself and for pragmatism, Sora was thanking him anyway.
In the third story, the talks with the various characters as Alex tries to get over Erica's betrayal and death.
The reunion with Alex in the third story as well as the scene when the Official Couple became, well, official.
The Re:Coded fic basically emphasises the relationship described in the moment mentioned at the top of the page: even though Alex can be selfish and unhelpful, Sora is aware of it, Sora is aware that Alex is also aware of it, and Sora offers his friendship and trust anyway because, in Data Alex's words, Sora is a good friend to have.