Paul makes some good points in his post on sedition, though the abuses of the Palmer raids and the excesses of Wilson's wartime government in particular should be remembered for their overreaching and paranoia. Wilson made a habit of jailing legitimate critics of the war, and fostered an atmosphere in which calls for the arrest of Sen. La Follette, for example, were commonplace.
I would follow up by noting what I think is still a relatively little-known fact: Jefferson objected to the Alien and Sedition Acts in large part on account of their redundancy and encroachment on the rights of the states. State laws c. 1798 already outlawed sedition, and Jefferson framed his protests against the Acts as a defense of state sovereignty. In other words, one of the basic problems Republicans had with the federal legislation on sedition in particular was that it was an act by the federal government in an area where it lacked authority and after the states had already addressed at least part of the problem. It was not ultimately a defense of seditious speech in the name of freedom of speech, but a protest against perceived encroachment by the center against the states. The complaint about the federal legislation fit into Jefferson's general anxiety about Federalist "monocracy" and his pamphleteering and propaganda struggle against what he regarded as Federalist usurpation (mostly related to the fight over the Bank).
One of the reasons for the generally poor memory of Adams' administration over the years is that the Quasi-War has never struck the popular imagination as a particularly serious or important conflict (and it was admittedly a minor, essentially entirely naval war that had limited impact on most citizens), which makes what were effectively wartime measures seem more unnecessary and excessive than they, in fact, were. The Republicans of the period did not distinguish themselves as good judges in their sympathy for the Revolution. It is impossible to separate the reaction of the Adams administration from the episodes involving the breakdown in relations with France and earlier attempts to draw America into the war on France's side that preceded the final rupture. Under the circumstances, and in light of what President Jefferson actually did once he was in power and was enforcing the Embargo Act, we can be fairly impressed by the restraint shown by Adams.