It depends on what aspects of the reformation you want to talk about- theologically, religion became both more and less of a state issue. On the one hand, states were no longer bound by the Papacy as they were previously; however, the conflicts regarding each prince and duke's religion would be the impetus for the 30 years war, possibly the most important war in european history.

Politically, the reformation wreaked havoc upon the authority of the Hapsburgs and the Holy Roman Empire. It was perhaps the only impetus with the inherent ability to cease Hapsburg dominion under Charles V. Even then, if not for the Ottoman Empire's advances into Hungary and Austria, Charles may have still been able to keep it under heel for a while longer, politically. The inability of Charles to subdue rebellious protestant kingdoms proved irrevocably damaging for the Empire- the split between the protestant north and Catholic south, along with long simmering tensions in Bohemia, proved plenty to spark the 30 years war 100 years later. The 30 years war proved the ultimate end of Papal secular authority- for the first time in memory, neither the Pope or a papal legate would preside over major peace talks. And when the Pope condemmned the Peace of Westphalia for being heretical, he was blithely ignored.

Of course, religion still played an important role from this point on, particulalry in the English civil war, and Louis XIV's Edict of Fontainblue, but it seemed much more about public stability and less about actual salvation of the masses.