Are 2-handed weapons ever worth it?

You're looking at DPS, not Damage, right?

Two Handers tend to be slower - you attack much less frequently - but hit much harder. This is particularly useful in combination with the way several channelled or high-cost skills work - you'll conserve your resources more while doing comparable damage with a big heavy weapon, at the cost of defense, or possibly some extra damage. You'll also want to take a look at this question for a rundown on dual wield mechanics:

How is listed DPS calculated when dual-wielding weapons?

(Your class also comes in to play here. For example, Demon Hunters using a 2h such as a Bow instead of a Hand Crossbow can still equip a Quiver in the OH, retaining the stat bonuses from the offhand slot).

The 2-hander I'm currently using is ~25% higher in DPS than anything else I've found, and it's rare so it has as many affixes as two normal weapons would have.

I think it all depends on what you find in your travels.

Some spells or auras rely on having a to hander equipped. For instance there is a monk passive that improves spirit regeneration rate when you have a two hander equipped. If damage isn't the only concern, two handers do have a place.

You do not attack with both 1 handers at the same time. You alternate, and thus each of your weapon-based damage skills are weaker since the weapon damage on each 1 hander is less than a 2 hander. The advantage, however, is that 1 handers are faster, so any skills that have proc (trigger) abilities, such as chance to stun/crit/slow/poison, will occur more often with 1 handers. Furthermore, in the case of demon hunter for example, you will generate hatred more quickly (though one might argue you also spend it faster). Experiment, and find out.