The Italian Wars dominated Europe politically around this time period (well, they started around 1494). Charles VIII (I believe, I don't have any books at my disposal) led French armies across the Alps into Italy to war with various city states (aligning himself, of course, with other city states); Spain under Ferdinand and Isabella was also involved, if I remember correctly (at least in Sicily).
The turn of the sixteenth century (and the Italian wars) saw the beginnings of the decline of the Italian city-states as the movers-and-shakers of Europe and the rise of the larger states such as France, England, and the Holy Roman Empire (under Charles V, this would include Spain and most of Germany, as well as his possessions in the New World...He was undoubtedly the most prolific landowner in European history).
The religious wars, however, had not yet started, and really don't until the Schmalkaldic Wars of the 1540s-1550s; there were various uprisings, however, tied to religious sentiments, such as with the Hussites, but these had been occuring over the course of the 15th century. The Chuch had a pretty decent hold on the polities of Europe at this point, but its temporal power waned considerably around this time (reaching a low-point in 1527).
I hope some of this information might prove useful. I suggest picking up a copy of Charles V by Karl Brandi or a history of the Catholic Church (finding something by Jedin would be marvelous).
Keith