I'll take a shot at this, but I'm sure others will have more to add. I should also note that I'm sure there are people out there that disagree that it's a distinct unit for very valid reasons.
The discovery of the "New World." For the first time, the geographic scope of the world was known to Europeans. Additionally, the colonization of the Caribbean (and later other parts of the Americas) led to the creation of a distinctly modern institution of slavery. Furthermore, it was on the backs of these slaves that we see the development of the sugar industry, the first major LARGE SCALE commodity (we can debate this if you like).
The reformation shattered the religious unity of Latin Europe. Yes, Latin Christianity was very diverse in the Middle Ages, as well as fractious and not always as unified as the Papacy would like, but the Reformation was more significant than any other religious schism (barring that between Latin and Orthodox Christianity).
The monarchs of the major polities had achieved a greater degree of centralization than they had before. While this was a continuation of medieval developments, I don't have a major problem pointing to a distinctly early modern monarchical form. Additionally, absolutism and constitutional monarchies were early modern developments.
Finally, I put the end of the early modern period at 1789 with the French Revolution. This was the beginning of the end for the nobility of Europe to a large degree and nationalism developed from this conflict (even if it had been germinating before hand). Additionally, by 1789, the industrial revolution was spinning into motion, ushering in drastic social, economic, and political changes.