The Collaborative International Dictionary of English v.0.48:

Molecule \Mol"e*cule\, n. [Dim. fr. L. moles a mass: cf. F.
   mol['e]cule. See 3d Mole.]
   1. One of the very small invisible particles of which all
      ordinary matter is supposed to consist.
      [1913 Webster]

   2. (Physics) The smallest part of any substance which
      possesses the characteristic properties and qualities of
      that substance, and which can exist alone in a free state.
      [1913 Webster]

   3. (Chem.) A group of atoms so united and combined by
      chemical affinity that they form a complete, integrated
      whole, being the smallest portion of any particular
      compound that can exist in a free state; as, a molecule of
      water consists of two atoms of hydrogen and one of oxygen.
      Cf. Atom.
      [1913 Webster]

WordNet (r) 3.0 (2006):

molecule
    n 1: (physics and chemistry) the simplest structural unit of an
         element or compound
    2: (nontechnical usage) a tiny piece of anything [syn: atom,
       molecule, particle, corpuscle, mote, speck]

Moby Thesaurus II by Grady Ward, 1.0:

138 Moby Thesaurus words for "molecule":
   Kekule formula, ace, acid, acidity, agent, air, alkali, alkalinity,
   alloisomer, anion, antacid, atom, atomic cluster, atomic particles,
   base, benzene ring, biochemical, bit, branched chain, brute matter,
   building block, cation, chain, chemical, chemical element,
   chromoisomer, closed chain, component, compound, compound radical,
   constituent, copolymer, cycle, dab, dimer, dole, dot, dram,
   dribble, driblet, dwarf, earth, electron, element,
   elementary particle, elementary unit, farthing, fire, fleck,
   flyspeck, fragment, fundamental particle, gobbet, grain, granule,
   groat, hair, handful, heavy chemicals, heterocycle, high polymer,
   homocycle, homopolymer, hydracid, hyle, hypostasis,
   inorganic chemical, ion, iota, isomer, jot, lattice, little,
   little bit, lota, macromolecule, material, material world,
   materiality, matter, meson, metamer, minim, minimum, minutiae,
   mite, modicum, monad, monomer, mote, natural world, nature,
   neutralizer, nonacid, nuclear particle, nutshell, organic chemical,
   ounce, oxyacid, particle, pebble, physical world, pinch, pittance,
   plenum, point, polymer, proton, pseudoisomer, quark, radical, ray,
   reagent, ring, scruple, side chain, simple radical, smidgen,
   smitch, space-lattice, speck, spoonful, spot, straight chain,
   stuff, substance, substratum, sulfacid, the four elements,
   thimbleful, tiny bit, tittle, trifling amount, trimer, trivia,
   unit of being, water, whit



The Devil's Dictionary (1881-1906):

MOLECULE, n.  The ultimate, indivisible unit of matter.  It is
distinguished from the corpuscle, also the ultimate, indivisible unit
of matter, by a closer resemblance to the atom, also the ultimate,
indivisible unit of matter.  Three great scientific theories of the
structure of the universe are the molecular, the corpuscular and the
atomic.  A fourth affirms, with Haeckel, the condensation of
precipitation of matter from ether -- whose existence is proved by the
condensation of precipitation.  The present trend of scientific
thought is toward the theory of ions.  The ion differs from the
molecule, the corpuscle and the atom in that it is an ion.  A fifth
theory is held by idiots, but it is doubtful if they know any more
about the matter than the others.