When Saber and Avenger attempt to use their Noble Phantasms against each others, both end up gruesomely injured by the interruption of Gilgamesh. Ben, who was then fighting Rider, panics, leaves the fight to check if his Servant is alright, and, when finding out, immediately retreats so he can heal her. All of this switching form twice to find her and then take her away from the battle quicker (keep in mind that it was implied in Alien Force that switching aliens repeatedly can cause the Omnitrix to run out of energy quicker, and two potential enemies were around, so he was taking risk by doing this). You can tell he really cares about her.
Then cut to Shirou doing the same with Saber, who admits in her thought she finds him surprisingly nice compared to Kiritsugu. Much to her dismay, it's immediately followed by a Moment Killer from Rin.
Also, Ben buying a snack to Avenger after she told him she never really ate much more than bread in her life:
Avenger: "Ben, this is too much. You shouldn't be wasting money like this. I am just a Servant and-"
Ben: "Relax, it's all being taken care of, let's just enjoy ourselves"
Ben hanging out with Ilya and getting her a stuffed animal at the Arcade. Really helped by Illya's cute mannerism.
Also, after Ben squashed Berserker to prevent him from killing Shirou, Illya is pissed off at him. As she is yelling at him, he finally calm her down with this:
Ben: "But I'd do the same for you just as quick Illya. We're friends after all. Or at least I hope we still can be."
Illya (smiling slightly): "I suppose... Okay Ben-niichan, if you promise not to take any more of Berserker's lives and not mess up our fights on purpose, I promise not to attack other Masters."
Avenger's reaction to Ben's injuries from Archer; also count as a Funny Moment, but still, it shows how much she cares about him as well. She actually was terrified by the mere fact he required to summon her, because that would mean he was in a situation he couldn't handle himself despite his powers.
Paradox saving Bazett and giving her a chance to get Lancer back.
Ben asks Kuzuki his reason to fight in the war:
Kuzuki: "If you are referring to the Grail, I care nothing for it. All I care for is right here." (holds Caster's hand)
This exchange between Rider and Avenger while Ben is fighting True Assassin:
Rider: "Aren't you worried for your Master?"
Avenger: "It would be insulting of me to worry for him. It would be as if I had little faith in his skills."
Ben helping Shirou get an unconcious Saber back home, with the two bonding and finding out how similar they are.
Even better is that, after it's done, Avenger asks Ben why he didn't just seize the occasion to get rid of Saber. Ben, of course, answers he doesn't go with tactic like that... and Avenger admits she didn't suggested it because she actually agrees with him.