The Freshman: When Buffy finds Olivia wearing Giles' shirt, she gets flustered and upset - and in many B/G fans' opinion, she's clearly both jealous and protesting *way* too much. Giles encourages her to be more independent, and she spends the rest of the season trying to do just that, to the detriment of their relationship.
The Harsh Light of Day: The image of Giles trying to reach Buffy while she's in bed with Parker is a powerful indication that she's making a big mistake. Later in the episode, Giles treats her claim to be an independent (and sexual) adult as too obvious to bother discussing. And when Buffy wants to give Angel the Gem of Amara, Giles tries to keep his face carefully neutral. He clearly disagrees with her decision, but he respects her right to make it.
Pangs: "You don't have a ricer?!" Apart from the funny seige and mayhem, Pangs was also enjoyable from a B/G perspective for all of its coupley, domestic, heads-of-the-household fun.
A New Man: Beside herself at the of something happening to Giles (and ready to wreak bloody vengeance on the demon that hurt him), Buffy sees Giles through his Fyarl exterior by looking into his eyes. Of course, this comes *after* she stabs him, but... no harm, no foul, right? (^_-)
Who Are You?: When Faith pulls a body switch, Giles asks Buffy to let him tie her up until he can verify her story, but she tells him that she doesn't have time for 'bondage fun'. At which point Buffy/Giles 'shippers everywhere burst out giggling. (And by the way, "What's a stevedore?")
The Yoko Factor: On a mission to separate the Scoobies, Spike knows exactly what buttons to push. Taunting Giles about needing to speak with the "lady of the house", Spike plays on Giles' growing fear that Buffy no longer needs him.
Restless: The 'meaning' of the opening scene of Giles' dream is open to interpretation (what with this being Restless and all), but his pointed reference to "the way men and women have behaved since the beginning" raised more than a few B/G shippers' eyebrows when the only other furniture visible in his flat was the bed upstairs.