Q:

Does damage reduction nullify sneak attack damage as a "special effect"? 

The DMG states (p.292):

"Whenever damage reduction completely negates the damage from an
  attack, it also negates most special effects that accompany the
  attack, such as injury type poison, monk's stunning or injury
  inflicted disease." 

Example: Rogue with 4d6 sneak hits flanked foe (DR: 10/-) with Medium dagger (dmg.  1d4).  Does he
a) ...trigger a sneak attack and deal 1d4+4d6-10 damage? 
b) ...deal no damage as sneak attack is a "special effect" negated along with his original damage? 
I know this has been answered for Pathfinder but apparently 3.5 rules seem to be different in this regard. 

A:

D&D 3.5 and Pathfinder rulings are the same on this subject. 
Sneak Attack damage is a bonus damage of the same kind as weapons damage and is actually a part of your weapon damage.  In regard of DR the wording is the same as for Str bonus, which is also a bonus damage. 
Your option a is generally correct. 
But it may be relevant in your case, that minimum damage rule doesn't apply when DR is involved. 
As for your quote, special effect must state in it's description that it depends on damage dealt.  Not to mention Sneak Attack is hardly a special effect of a kind similar to those listed in the quote.