This list is so bare it's depressing. Here's some more stories, but really, this page should be at least 10 pages long just for the past 12 years. Hell, reading a Noam Chompsky book or two will give you even better material going back before the 60's through the 90's.
2001-2011: A decade of civil liberties’ erosion in America http://www.civilfreedoms.org/?p=7260
The 10 most outrageous civil liberties violations of 2006. http://www.slate.com/articles/news_and_politics/jurisprudenc...
Are we becoming a police state? Five things that have civil liberties advocates nervous http://www.pbs.org/wnet/need-to-know/the-daily-need/are-we-b...
Obama crushes civil liberties like Bush never did http://www.wnd.com/2012/03/obama-crushes-civil-liberties-lik...
For a brief look back in history: Who is the worst civil liberties president in US history? http://www.guardian.co.uk/commentisfree/2012/nov/02/obama-ci...