If civil liberties is the point of discussion, then two cases must be put at the head of the list.  Plessy v Ferguson (1896) and Brown v. Board of Ed. (1954).  In Plessy, the court had held that certain southern state and local laws establishing segregation in public facilities (schools, bathrooms and the like) were constitutional; so long as the facilities in question were "separate but equal." The court never defined the term "equal" by the way; which led to the next 50 or so years of history in the south being a segregated history.  Brown v Board, of course overturns the Plessy case... although once again, the court failed to express their legal meaning in their decision; saying that the state governments had to desegregate in a "timely fashion."

I would include Schenck v. US (1919) in any discussion of important civil liberties cases. In this case the Court ruled that speech that posed a "clear and present danger" to the security of the United States was not protected by the First Amendment. It established, in other words, a test for determining the limits of First Amendment protections for free speech. The case stemmed from the prosecution of Socialist Party official Charles Schenck under the Espionage Act of 1917, a measure designed to squelch dissent during World War I. Schenck had been circulating literature that encouraged Americans to resist the draft. 

Mapp v. Ohio has to be one of the most important.  This is the case that applied the exclusionary rule to state governments.  That rule serves as one of the major ways in which our civil liberties (mainly the right against unreasonable searches and seizures) is protected.