Germany and the Holy Roman Empire by Joachim Whaley is an excellent two-volume history of the HRE and Central Europe.

Germany under the Old regime, 1600-1790 by John G Gagliardo is an older survey, but still a useful one. The life of the Burger was an essential component of old regime Germany and German Home Towns: Community, State, and General Estate, 1648-1871 by Mack Walker examines this evolution of the German town over the longue duree.

Although Ozment is an important figure in EME historiography, he is very much a cheerleader for the Reformation. Ulrike Strasser's State of Virginity: Gender, Politics, and Religion in a Catholic State is an accessible entry into the world of Catholic Reformation Germany. The works of Thomas Robisheaux (Rural Society and the Search for Order and The Last Witch of Langenburg: Murder in a German Village) show a Protestant Reformation that was much more disorganized and chaotic than the one Ozment presents. Power in the Blood: Popular Culture and Village Discourse in Early Modern Germany by David Sabean also examines the nature of village life.

One frustrating problem with Central European history in the Early Modern Era historiography is that all roads lead to (or from) Luther. While the Reformation was an important facet of Central European life, it was not the only thing going on at this time. Christine Johnson's The German Discovery of the World: Renaissance Encounters with the Strange and Marvelous is an excellent corrective to this as she shows how German perceived their connection to the emerging Atlantic world. The Utility of Splendor: Ceremony, Social Life, and Architecture at the Court of Bavaria, 1600-1800 examines how issues of space and architecture were reflections of power. Bacchus and Civic Order: The Culture of Drink in Early Modern Germany by B. Ann Tlustly is another example of reconceptualizing the "Reformation in the Cities" approach pioneered by Ozment and exploring the cultural and social intersections of religion and daily life in the city of Augsburg.

A Concise History of Germany, Piety and Politics: Religion and the Rise of Absolutism in England, Wurttemberg and Prussia Both by ~ Mary Fulbrook.

The Burgermeister's Daughter: Scandal in a 16th Century German Town, Flesh and Spirit: A Study of Private Life in Early Modern Germany, A Mighty Fortress: A New History of the German People, The Serpent and the Lamb: Cranach, Luther, and the Making of the Reformation, When Fathers Ruled: Family Life in Reformation Europe all by ~ Steven Ozment.

Fulbrook & Ozment have authored many books on all aspects & areas of German History. You can read about them & all their published books here; Fulbrook, Ozment

For the earlier early modern era:

Thomas Brady, German Histories in the Age of Reformations, 1400-1650

Tom Scott, Society and Economy in Germany, 1300-1600

Peter Wilson, who wrote the well-received The Thirty Years' War: Europe's Tragedy, has a 1000 page history of the Holy Roman Empire coming out in February 2016 called Heart of Europe: A History of the Holy Roman Empire.

If you are new to the subject, however, Wilson probably shouldn't be your first choice.

Germany and the Holy Roman Empire by Whaley. It comes in two volumes with the first one ranging from 1493 to 1648 and the second one ranging from 1648 to 1806.

German Peasant's War:

The Revolution of 1525: The German Peasants' War from a New Perspective, Peter Blickle

The German Peasants' War and Anabaptist Community of Goods, James M. Stayer

The German Peasant War of 1525: New Viewpoints, Bob Scribner (collection of essays)

The German Reformation and the Peasants' War: A Brief History with Documents, Micheal G. Baylor (mostly a sourcebook)

While not an academic work, Osprey Publishing's Man at Arms series has a book for the Peasant's War that is useful for visualizing the kind of combat and the equipment used.