The Collaborative International Dictionary of English v.0.48:

Manipulate \Ma*nip"u*late\, v. i.
   To use the hands in dexterous operations; to do hand work;
   specifically, to manage the apparatus or instruments used in
   scientific work, or in artistic or mechanical processes;
   also, specifically, to use the hand in mesmeric operations.
   [1913 Webster]

The Collaborative International Dictionary of English v.0.48:

Manipulate \Ma*nip"u*late\, v. t. [imp. & p. p. Manipulated;
   p. pr. & vb. n. Manipulating.] [LL. manipulatus, p. p. of
   manipulare to lead by the hand, fr. L. manipulus. See
   Maniple.]
   1. To treat, work, or operate with the hands, especially when
      knowledge and dexterity are required; to manage in hand
      work; to handle; as, to manipulate scientific apparatus.
      [1913 Webster]

   2. To control the action of, by management; as, to manipulate
      a convention of delegates; also, to manage artfully or
      fraudulently; as, to manipulate accounts, or election
      returns; to manipulate the stock market.
      [1913 Webster]

WordNet (r) 3.0 (2006):

manipulate
    v 1: influence or control shrewdly or deviously; "He manipulated
         public opinion in his favor" [syn: manipulate, pull
         strings, pull wires]
    2: hold something in one's hands and move it
    3: tamper, with the purpose of deception; "Fudge the figures";
       "cook the books"; "falsify the data" [syn: fudge,
       manipulate, fake, falsify, cook, wangle,
       misrepresent]
    4: manipulate in a fraudulent manner; "rig prices" [syn: rig,
       manipulate]
    5: control (others or oneself) or influence skillfully, usually
       to one's advantage; "She manipulates her boss"; "She is a
       very controlling mother and doesn't let her children grow
       up"; "The teacher knew how to keep the class in line"; "she
       keeps in line" [syn: manipulate, keep in line, control]
    6: treat manually, as with massage, for therapeutic purposed

Moby Thesaurus II by Grady Ward, 1.0:

124 Moby Thesaurus words for "manipulate":
   abuse, adulterate, angle, barnstorm, be responsible for, beguile,
   bleed, bleed white, call the signals, captain, carry on, carry out,
   carry through, choreograph, come in contact, command, conduct,
   contrive, control, cook, copilot, deal with, direct, dispense,
   do with, doctor, drain, drive, employ, engineer, exercise, exert,
   exploit, fake, falsify, feel, feel of, fiddle, finagle, finesse,
   finger, flick, fly, gerrymander, govern, handle, head, head up,
   ill-use, impose upon, influence, intrigue, jockey, juggle, lead,
   lead on, load, machinate, make go, make the rules, make use of,
   manage, maneuver, mastermind, milk, misuse, negotiate, officer,
   operate, orchestrate, order, pack, palm, palpate, paw, peel off,
   perform on, pilot, plant, play, play games, play on, plot, ply,
   poke at, practice, prescribe, presume upon, prod, pull strings,
   pull the strings, quarterback, regulate, retouch, rig, run, salt,
   scheme, see to, skipper, solo, sophisticate, stack, steer, stroke,
   suck dry, swing, take advantage of, take care of, take command,
   take the lead, tamper with, tap, thumb, touch, twiddle, use,
   use ill, utilize, wangle, wield, work, work on, work upon