Sherry makes Jake promise that if Simmons turns out to be a traitor and the rendezvous is a trap, regardless of what happens to her, he will run. When time comes, however...
Sherry: You promised!
Jake: I lied.
After defeating Ustanak in Jake's final chapter:
Jake: You saved me. You know that, don't you?
At the beginning of their campaign, Jake asks for $50 million for his world-saving blood. In their ending, Jake texts Sherry saying that he lowered the price to $50.
In Leon's final chapter, he protects an unconscious Ada from a mutating Simmons, going so far as to shield her from a hail of spikes with his own body. When Ada wakes up she gives a sarcastic remark, but she also touches Leon's hand on her shoulder, like a silent little thank you. The dialogue and the context makes it even more heartwarming, though; Leon had recently been told Ada was dead, and while she's knocked out, he tells her that if she's the real Ada, she can pull through. The relief in Leon's voice when he makes his own sarcastic joke in response seals it. The whole scene is reminiscent of their final scenes together at the climax of Resident Evil 2.
Helena being exonerated at the end of the campaign, after being hell-bent on avenging Deborah and was willing to turn herself in after defeating Simmons.
After spending a good portion of the game acting cold towards Piers, Chris tells him he would be honored if Piers took over his role in the BSAA once Chris retires. Sadly, things don't turn out that way.