O boy. Go go gadget wall-of-text!
Aright, damage reduction has its roots in the old days of advanced D&D where monsters were outright immune to weapons under a certain degree of enchantment. This in turn was based off of Lord of the Rings "Return of the King" where the Lich King of Angmar was hamstringed by a hobbit using ione of the old barrow blades that the party had acquired after their encounter with the wight just before they were rescued by Tom Bombadil (a series of events that were removed ostensibly to save movie running time but more likely to prevent moviegoers from being traumatized by the sight of four hobbits streaking through grassy fields under the supervision of a magical hermit. Too many things wrong with that scene).
Background aside, the blade was of exceeding quality, and "a lesser blade, even driven by a mightier arm, could not have dealt so vicious a blow." From this, the idea of damage reduction was drawn.
If you are worried about DR as a means by which to prevent the BBEG from being nibbled to death by a swarm of ducks wielding natural 20's consider one of the following options:
1) For each magical "plus" of the weapon, reduce the damage reduction provided by 20% (from DR x/magic), to where the magical DR is negated completely only by a +5 enhancement bonus weapon. I've found this house rule nips a lot of minmaxing of weapon fluff bonuses VERY quickly.
2) Armor provides DR as well as armor bonus. Apply some of the damage prevented this way to the armor. Gives a good reason for the fighter to want to wear scale mail instead of streaking with the wizard's Mage Armor, and gives the base Fighter a chance to survive ye olde Grand Master Fists of Flurry-San who is facing off against him with Bracers of Armor +8. (Another time I will get into my rant against the ludicrous damage dice afforded to unarmed monks, but not today)
3) natural 20's do not afford an automatic hit should your bonuses not add up t the AC, they just grant you another attack roll with a +19, cumulatively if necessary. This turns a flat 5% chance to hit into something far more realistic- it's feasible for a single peasant to get a lucky shot in, but not so often as 1 in 20. Especially not against something that's rocking a 35 AC.
Just some food for thought.
-Axenme1's wall of text crits you for OVER 9000!!!