The Collaborative International Dictionary of English v.0.48:

Compunction \Com*punc"tion\, n. [OF. compunction, F.
   componction, L. compunctio, fr. compungere, compunctum, to
   prick; com- + pungere to prick, sting. See Pungent.]
   1. A pricking; stimulation. [Obs.]
      [1913 Webster]

            That acid and piercing spirit which, with such
            activity and compunction, invadeth the brains and
            nostrils.                             --Sir T.
                                                  Browne.
      [1913 Webster]

   2. A picking of heart; poignant grief proceeding from a sense
      of guilt or consciousness of causing pain; the sting of
      conscience.
      [1913 Webster]

            He acknowledged his disloyalty to the king, with
            expressions of great compunction.     --Clarendon.

   Syn: Compunction, Remorse, Contrition.

   Usage: Remorse is anguish of soul under a sense of guilt or
          consciousness of having offended God or brought evil
          upon one's self or others. Compunction is the pain
          occasioned by a wounded and awakened conscience.
          Neither of them implies true contrition, which denotes
          self-condemnation, humiliation, and repentance. We
          speak of the gnawings of remorse; of compunction for a
          specific act of transgression; of deep contrition in
          view of our past lives. See Regret.
          [1913 Webster]

WordNet (r) 3.0 (2006):

compunction
    n 1: a feeling of deep regret (usually for some misdeed) [syn:
         compunction, remorse, self-reproach]

Moby Thesaurus II by Grady Ward, 1.0:

81 Moby Thesaurus words for "compunction":
   attrition, bashfulness, beef, better self, bitch, boggle, boggling,
   boycott, challenge, complaint, conscience, conscientiousness,
   contriteness, contrition, demonstration, demur, demurral, demurrer,
   diffidence, disinclination, exception, expostulation, falter,
   faltering, fear, grievance, grievance committee, hesitance,
   hesitancy, hesitation, howl, indignation meeting, kick, march,
   misgiving, modesty, nonviolent protest, objection, pangs,
   pangs of conscience, pause, penance, penitently, picketing,
   pricking of heart, protest, protest demonstration, protestation,
   punctiliousness, qualm, qualm of conscience, qualmishness, qualms,
   rally, recoil, regret, reluctance, remonstrance, remonstration,
   remorse, repentance, reserve, rue, ruth, scruple, scruples,
   scrupulosity, scrupulousness, self-reproach, shrinking, shyness,
   sit-in, squawk, stickling, strike, teach-in, throes,
   touch of conscience, twinge of conscience, unwillingness,
   voice of conscience