The Collaborative International Dictionary of English v.0.48:

Punctuate \Punc"tu*ate\, v. t. [imp. & p. p. Punctuated; p.
   pr. & vb. n. Punctuating.] [Cf. F. ponctuer. See
   Punctual.]
   To mark with points; to separate into sentences, clauses,
   etc., by points or stops which mark the proper pauses in
   expressing the meaning.
   [1913 Webster]

WordNet (r) 3.0 (2006):

punctuate
    v 1: insert punctuation marks into [syn: punctuate, mark]
    2: to stress, single out as important; "Dr. Jones emphasizes
       exercise in addition to a change in diet" [syn: stress,
       emphasize, emphasise, punctuate, accent,
       accentuate]
    3: interrupt periodically; "Her sharp questions punctuated the
       speaker's drone"

Moby Thesaurus II by Grady Ward, 1.0:

95 Moby Thesaurus words for "punctuate":
   accent, accentuate, analyze, belabor, blaze, blaze a trail,
   blemish, blotch, bracket, brand, break, chalk, chalk up, check,
   check off, cicatrize, conjugate, dapple, dash, decline, define,
   delimit, demarcate, discolor, divide, dot, dwell on, emphasize,
   engrave, fleck, freckle, gash, give emphasis to, harp on, hatch,
   highlight, hyphenate, impress, imprint, inflect, interrupt,
   intersperse, italicize, line, make a mark, mark, mark off,
   mark out, mottle, nick, notch, overaccentuate, overemphasize,
   overstress, parenthesize, parse, pencil, pepper, place emphasis on,
   point, point up, prick, print, punch, puncture, riddle, rub in,
   scar, scarify, score, scotch, scratch, seal, seam, separate, speck,
   speckle, splotch, spot, spotlight, sprinkle, stain, stamp, star,
   stigmatize, streak, stress, striate, stripe, tattoo, tick,
   tick off, trace, underline, underscore