I'm tempted to say Jenny, but I remeber how Giles acted toward her after he and buffy learned of her Gypsy spying. They did overcome that, however. Just in time for Angelus to, well you know.
Giles had that pleasantly awckward deal with Joyce while they were under the influence of the demonic willy wonka, but they almost seemed embarresed by it in retrospect. They had a fun chemestry as reckless youths, but how different are they now as adults? I would think if they had those kind of mutual feelings for each other beyond friends, they would have hooked up sober.
I would have loved to see a Joyce and Giles 'true couple', but I don't think it ever actually happened short of altered behavior to a degree that it actually made me like Snyder. 🙂
Giles could forgive betrayal by Jenny, but could not get over his own weirdness concerning "love ala cop car." with Joyce. I sooo wanted him to get together with Joice, Jenny was dead and like others have said what a couple! but it never happened.
I think Giles would have prefered Jenny over Joyce.