The Supreme Court has decided 5 to 4 that alien terrorists held in a foreign country, namely Cuba, by the U.S. have certain legal rights comparable to those of a U.S. citizen. An article concerning the implications can be seen here.
The case, Boumediene v. Bush, certainly represents a low point in the common sense application of law to problems facing our nation. What it does show is that five Supreme Court Justices have forgotten the lessons of 9/11 and no longer believe us to be "at war."
I suspect the short-term practical implication may be that in places like Afghanistan U.S. troops will be less willing to take prisoners and more willing to leave enemy combatants dead where encountered. Whether such behavior serves U.S. interests is less clear.