The Collaborative International Dictionary of English v.0.48:

discombobulate \discombobulate\ v.
   to cause to be confused; confuse emotionally.

   Syn: confuse, flurry, consternate, disconcert, put off,
        bewilder, bemuse, throw.
        [WordNet 1.5]

WordNet (r) 3.0 (2006):

discombobulate
    v 1: cause to be confused emotionally [syn: bewilder,
         bemuse, discombobulate, throw]
    2: be confusing or perplexing to; cause to be unable to think
       clearly; "These questions confuse even the experts"; "This
       question completely threw me"; "This question befuddled even
       the teacher" [syn: confuse, throw, fox, befuddle,
       fuddle, bedevil, confound, discombobulate]

Moby Thesaurus II by Grady Ward, 1.0:

59 Moby Thesaurus words for "discombobulate":
   addle, addle the wits, agitate, ball up, becloud, bedazzle,
   befuddle, bewilder, bother, bug, cloud, confuse, daze, dazzle,
   discomfit, discompose, disconcert, disorganize, disorient,
   disquiet, distract, disturb, electrify, embarrass, entangle,
   flummox, flurry, fluster, flutter, fog, fuddle, fuss, jar, jolt,
   maze, mist, mix up, moider, muddle, mull, perplex, perturb, pother,
   put out, raise hell, rattle, rock, ruffle, shake, shake up, shock,
   stagger, stir, throw into confusion, throw off, trouble, unhinge,
   unsettle, upset