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]