The Collaborative International Dictionary of English v.0.48:

Stain \Stain\ (st[=a]n), v. t. [imp. & p. p. Stained
   (st[=a]nd); p. pr. & vb. n. Staining.] [Abbrev. fr.
   distain.]
   1. To discolor by the application of foreign matter; to make
      foul; to spot; as, to stain the hand with dye; armor
      stained with blood.
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   2. To color, as wood, glass, paper, cloth, or the like, by
      processes affecting, chemically or otherwise, the material
      itself; to tinge with a color or colors combining with, or
      penetrating, the substance; to dye; as, to stain wood with
      acids, colored washes, paint rubbed in, etc.; to stain
      glass.
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   3. To spot with guilt or infamy; to bring reproach on; to
      blot; to soil; to tarnish.
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            Of honor void,
            Of innocence, of faith, of purity,
            Our wonted ornaments now soiled and stained.
                                                  --Milton.
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   4. To cause to seem inferior or soiled by comparison.
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            She stains the ripest virgins of her age. --Beau. &
                                                  Fl.
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            That did all other beasts in beauty stain.
                                                  --Spenser.
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   Stained glass, glass colored or stained by certain metallic
      pigments fused into its substance, -- often used for
      making ornamental windows.
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   Syn: To paint; dye; blot; soil; sully; discolor; disgrace;
        taint.

   Usage: Paint, Stain, Dye. These denote three different
          processes; the first mechanical, the other two,
          chiefly chemical. To paint a thing is to spread a coat
          of coloring matter over it; to stain or dye a thing is
          to impart color to its substance. To stain is said
          chiefly of solids, as wood, glass, paper; to dye, of
          fibrous substances, textile fabrics, etc.; the one,
          commonly, a simple process, as applying a wash; the
          other more complex, as fixing colors by mordants.
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WordNet (r) 3.0 (2006):

stained glass
    n 1: glass that has been colored in some way; used for church
         windows