The Collaborative International Dictionary of English v.0.48:

Cipher \Ci"pher\, a.
   Of the nature of a cipher; of no weight or influence. "Twelve
   cipher bishops." --Milton.
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The Collaborative International Dictionary of English v.0.48:

Cipher \Ci"pher\, v. i. [imp. & p. p. Ciphered; p. pr. & vb.
   n. Ciphering.]
   To use figures in a mathematical process; to do sums in
   arithmetic.
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         'T was certain he could write and cipher too.
                                                  --Goldsmith.
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The Collaborative International Dictionary of English v.0.48:

Cipher \Ci"pher\, n. [OF. cifre zero, F. Chiffre figure (cf.
   Sp.cifra, LL. cifra), fr. Ar. [,c]ifrun, [,c]afrun, empty,
   cipher, zero, fr. [,c]afira to be empty. Cf. Zero.]
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   1. (Arith.) A character [0] which, standing by itself,
      expresses nothing, but when placed at the right hand of a
      whole number, increases its value tenfold.
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   2. One who, or that which, has no weight or influence.
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            Here he was a mere cipher.            --W. Irving.
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   3. A character in general, as a figure or letter. [Obs.]
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            This wisdom began to be written in ciphers and
            characters and letters bearing the forms of
            creatures.                            --Sir W.
                                                  Raleigh.
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   4. A combination or interweaving of letters, as the initials
      of a name; a device; a monogram; as, a painter's cipher,
      an engraver's cipher, etc. The cut represents the initials
      N. W.
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   5. A private alphabet, system of characters, or other mode of
      writing, contrived for the safe transmission of secrets;
      also, a writing in such characters.
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            His father . . . engaged him when he was very young
            to write all his letters to England in cipher. --Bp.
                                                  Burnet.
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   Cipher key, a key to assist in reading writings in cipher.
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The Collaborative International Dictionary of English v.0.48:

Cipher \Ci"pher\, v. t.
   1. To write in occult characters.
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            His notes he ciphered with Greek characters.
                                                  --Hayward.
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   2. To get by ciphering; as, to cipher out the answer.
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   3. To decipher. [Obs.] --Shak.
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   4. To designate by characters. [Obs.] --Shak.
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Moby Thesaurus II by Grady Ward, 1.0:

175 Moby Thesaurus words for "cipher":
   Aesopian language, Babel, Greek, John Hancock, X, a nobody,
   a nothing, add, algebraize, allegory, alphabetic character, argot,
   aught, autograph, babble, binary digit, bit, break, calculate,
   cant, cast, character, charactery, christcross, clear up, code,
   coded message, common man, compute, conventional symbol,
   countermark, countersign, countersignature, counterstamp, cross,
   cryptoanalysis, cryptoanalytics, cryptogram, cryptograph,
   cryptographer, cryptography, decipher, device, digit, divide,
   dope out, double Dutch, dud, dummy, emblem, encipher, encode,
   endorsement, estimate, extract roots, figure, figure in,
   figure out, figurehead, garble, gibberish, gift of tongues,
   glossolalia, gobbledygook, goose egg, graph, grapheme, hand,
   hollow man, iconology, ideogram, initials, insignificancy, integer,
   invisible ink, jackstraw, jargon, jumble, lay figure, letter,
   lexigraphic character, lightweight, little fellow, little guy,
   logogram, logotype, love knot, man of straw, mark,
   mark of signature, measure, mediocrity, monogram, multiply, nada,
   naught, nebbish, nichts, nihil, nil, nix, no such thing, nobody,
   nobody one knows, noise, nonentity, notation, nothing,
   nothing at all, nothing on earth, nothing whatever, nullity,
   number, numeral, numero, obscurity, phonetic character,
   phonetic symbol, pictogram, pictographic character, pip-squeak,
   punk, puppet, pushover, puzzle out, reckon, resolve, runt, score,
   scramble, scrub, seal, secret language, secret writing, shrimp,
   sigil, sign, sign manual, signature, signet, slang, small fry,
   small potato, small potatoes, squirt, squit, subscription,
   subtract, syllabic, symbol, symbolic system, symbolism,
   symbolization, symbology, sympathetic ink, take account of, tally,
   thing of naught, token, totem, totem pole, trifle, type, unravel,
   unriddle, visa, vise, whiffet, whippersnapper, whole number,
   work out, writing, written character, zero, zilch