...it's mentioned that at some time in the past, Gwaihir (the "Lord of the Eagles") had been wounded, shot with an arrow, and Gandalf found him and healed him, saving his life.  I suspect that this is the favor in question, although one might suppose the help the eagles gave to Thorin and Company, including Gandalf, might have constituted part of the repayment.  But perhaps this was repayment of a more personal kind, since you will note that the instances referred to in LotR are all either specifically for Gandalf's benefit, or done at his request.  In the Hobbit, the Eagles' rescue was their choice; they rescued the company from the goblins largely because they hated goblins, not because they were doing a favor for Gandalf (even though he was one of those saved).  And their part in the Battle of the Five Armies was also doubtless done for their own benefit, driven by their hatred for the goblins, not (as far as we know) because Gandalf asked for their aid.

Actually, if this question has come up, it hasn't been recently. :)

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