One of our alert former fellows brought Hillary Clinton's quotation of Jefferson during her recent Secretary of State confirmation hearings to my attention.  Of course I can't help myself from checking to make sure that famous people quoting TJ have actually gotten their quotes correct, because a) I'm a stickler, and b) someone else will surely ask about it. This one is a weird little documentary curiosity, as it turns out.  Jefferson did in fact write this, but only in a draft, which was later revised to exclude the portion that Hillary is quoting.  Jefferson's "Paragraphs for the President's Annual Message to Congress," which he prepared for George Washington in October 1792 at Washington's request, begins:

The interests of a nation, when well understood, will be found to coincide with their moral duties.  Among these it is an important one to cultivate habits of peace and friendship with our neighbors.  To do this we should make provision for rendering the justice we must sometimes require from them.  I recommend therefore to your consideration Whether the laws of the Union should not be extended to restrain our citizens from committing acts of violence within the territories of other nations, which would be punished were they committed within our own. - And in general the maintenance of a friendly intercourse with foreign nations will be presented to your attention by the expiration of the law for that purpose, which takes place, if not renewed, at the close of the present session. (Papers of Thomas Jefferson, 24:486; letterpress copy at Library of Congress)

That was the version of October 15, 1792.  Before Washington gave the address on November 6th, however, Jefferson sent Washington a new version, which read:

Instead of the paragraph 'The interests of a nation &c. --within our own,' formerly proposed, the following substitute is thought better. All observations are unnecessary on the value of peace with other nations.  It would be wise however, by timely provisions, to guard against those acts of our citizens, which might tend to disturb it, and to put ourselves in a condition to give that satisfaction to foreign nations, which we may sometimes have occasion to require from them.  I particularly recommend to your consideration the means of preventing those aggressions by our citizens on the territory of other nations, and other infractions of the law of Nations, which furnishing just subject of complaint, might endanger our peace with them. --And in general the maintenance &c.  (Papers of Thomas Jefferson, 24:552 - letterpress copy at Library of Congress)

Ford, bless his persnickety soul, does in fact note that Jefferson "suggested an alteration in this paper," and printed the text of the revised version. Although it's only clear in the Princeton edition of TJ's papers what, exactly, Washington ended up actually using. In the end, though, Hillary very cleverly phrased her quotation such that all the above particular-ness about drafts and revisions doesn't necessarily signify: "I take great comfort in knowing that our first secretary of state, Thomas Jefferson, also subscribed to that view, reminding us across the centuries: 'The interests of a nation, when well-understood, will be found to coincide with their moral duties.'" Jefferson did write this, and we're now reading it, so he is talking to us "across the centuries," whether he meant to or not.  I have noted this one for posterity in the TJ Encyclopedia - the article includes the full text of TJ's first draft (which is in fact rather boring - the most exciting part of the whole thing is the first sentence).