Put simply, just about every interaction between Ilya and Shirou either has or is one of these.
In Chapter 1: Shirou has just met Ilya, and has no idea of who she is, why she gave him a cryptic warning... nothing. Yet despite this - and an instinct screaming him that approaching her would be risking death - he reaches out to her. He puts on a big-brotherly expression, he offers to walk her home or lend her money for the bus service, he compliments the hair she inherited from her mother... and in the end, the part of Ilya that still yearns for affection wins over the ten years of cynicism drilled into her by the Einzberns.
In Chapter 6, he's out to get supplies for lunch (for Saber, among others), and runs into Ilya again. After some small talk, she asks - and then begs - him to give her a tour of the town just to spend time with her. Despite knowing he'll get in trouble if he delays getting back, he cannot resist the urge to make her happy. Following that...well:
The brief moment of shock at his acceptance, followed by the practical flood of joy into the girl's eyes as she latched onto his arm like a vice clamp, convinced Shirou that he had made the correct decision.
And then, he promises to meet her again tomorrow - and despite being sick from prana drain, he keeps his word.
In Chapter 14, Shirou meets Irisviel. She does not carry any emnity towards him or Kiritsugu for what Ilya went through the last ten years - she simply notes that he's been a miraculous influence on her little girl by giving her the affection she's been starved of, and asks him to do his best to save her. And though Shirou's unsure if he's dreaming or not, he accepts. Whether it's meant to be Ship Tease or not, it's beautiful to watch because either way, Iri seems to have accepted Shirou as her own.
Chapter 15: despite her misgivings about Ilya, Saber jumps in front of Gilgamesh's attempt to skewer her and blocks the sword he fired from Gate of Babylon. Even better in that she also defended Berserker (who had leapt in front of Ilya first) from the attack, and declared a no-strings-attached Enemy Mine with them, against Gil. Ilya is left stunned, and actually realises that Being Good Sucks might not quite be true.
Saber: "Perhaps Shirou is influencing me oddly, to defend a potential foe so. Or perhaps I am still simply curious as to what you know about the oddities in this War. But this Archer is no ally of mine, Lady Einzbern, and I do owe you a debt of assistance. If you stand against him, then I stand with you."
Gilgamesh: "I'm sorry? Did the meat puppet forget that she does not have permission to speak?"
Ilya: "That's wrong! If... you love someone, than... then doing anything that makes them sad should make you sad. And making them happy makes you happy. You... if you have to force them to love you back than it's just... it isn't right. They should love you because they love you!"
Saber: <smiles warmly> "Well-spoken, Lady Einzbern. Perhaps choosing to fight by your side was a better decision than I had imagined."
In Chapter 23, after Ilya lost Berserker, both Shirou and Saber pledge to act as her Servants as a form of penance (for Saber being forced to put down the possessed Servant. This causes her to blush in embarrassment, evidently moved and flattered by their (admittedly stupidin her mind) Honour Before Reason.