This post was, oddly enough, prompted by Age of Conan rather than WoW. But you get a similar situation in WoW as well.
Most hybrids I know maintain multiple sets, even if they have one main spec and one offspec. So what do you do if a single non-repeatable quest gives rewards for both main and offspec?
Obviously most people choose main spec. But what if the main spec upgrade would only be a slight upgrade, and the offspec upgrade is a large upgrade?
One theory is that you should keep your main spec as advanced as possible, even if that hurts your offspec. Another theory is that you should use quests to advance your offspec. Your main spec will get better rewards in instances and group content. After all, it's much easier to get healing items while you are a healer, rather than fight with DPS for DPS items.
(Note that I am only talking about situations where questing would provide roughly equal rewards to instance loot. Like levelling or maybe the Quel'Delar questline.)
The specific incident that started me thinking about it was from Age of Conan. My main character is a level 35-ish Conqueror, which is a 2H or dual-wield class. I'm playing as a 2H Conqueror. There are two group quests in a chain. Both reward good 2-Handers, with the second one being slightly better than the first. But the second quest also offers a choice of a really good 1H, which would be a larger upgrade for that set of mine. Yet, I'm not likely to ever actually use those weapons. The 2H would be used all the time.
Unless, of course, I decided to respec.
Ah well, just getting a group going in Age of Conan is pretty hard, so this might be a non-issue in the end.