“No matter that patriotism is too often the refuge of scoundrels. Dissent, rebellion, and all-around hell-raising remain the true duty of patriots.”

Song lyrics, Infidels (1983), Sweetheart Like You

On polls showing that many Americans would support a restriction of free speech especially if against speech held to be unpatriotic, in a speech to the Society of Professional Journalists (11 September 2004)

Various; earliest source The Use of Force in International Affairs http://www.worldcat.org/oclc/21414360 (Philadelphia: Friends Peace Committee, 1961), 6, and popularized by various users in the 1960s:
If what your country is doing seems to you practically and morally wrong, is dissent the highest form of patriotism?
Dissent is the highest form of patriotism http://wiki.monticello.org/mediawiki/index.php/Dissent_is_the_highest_form_of_patriotism_(Quotation), Thomas Jefferson Encyclopedia
Other form by historian Howard Zinn Dissent In Pursuit Of Equality, Life, Liberty And Happiness: An Interview With Historian Howard Zinn http://www.tompaine.com/Archive/scontent/5908.html by Sharon Basco, TomPaine.com http://TomPaine.com, July 03 2002 (The quote can be found in the first sentence of Mr. Zinn's first answer; nowhere in that article does Howard Zinn attribute that quote to Jefferson.):
While some people think that dissent is unpatriotic, I would argue that dissent is the highest form of patriotism.
Law professor Jim Lindgren of The Volokh Conspiracy has traced the possible origin of this saying back as far as the 11 November 1984 obituary of pacifist activist Dorothy Hewitt Hutchinson in the Philadelphia Inquirer, quoting a 1965 interview. The direct quote there is: "Dissent from public policy can be the highest form of patriotism," she said in an interview in 1965. "I don't think democracy can survive without it, even though you may be crucified by it at times." According to the professor's research http://volokh.com/posts/1146554363.shtml, the misattribution was popularized in the 1990's by ACLU president Nadine Strossen. Bill Mullins of the American Dialect Society did further research http://listserv.linguistlist.org/cgi-bin/wa?A2=ind0605A&L=ADS-L&P=R1297&I=-3.
Misattributed

Must We Go to War? (1937)

Czar Nicholas II
1905
Collected Tales, Sketches, Speeches, & Essays, 1891-1910 (1992) ed. Louis J. Budd

"The Jury System" (February 1890)
Context: In this, our land, we are called upon to give but little in return for the advantages which we receive. Shall we give that little grudgingly? Our definition of patriotism is often too narrow. Shall the lover of his country measure his loyalty only by his service as a soldier? No! Patriotism calls for the faithful and conscientious performance of all of the duties of citizenship, in small matters as well as great, at home as well as upon the tented field.

Source: The Prague Cemetery

Source: Testament of a Critic (New York: Alfred A. Knopf, 1931), p. 16