Yes it did, and the formal version was (drumroll, please....) you.

In Early Modern English, thou was the singular and you was the plural. Plural you came to be used as a polite form of address (similar to the French vous, which is also used for the plural), but over time this polite form became more and more common, eventually displacing the singular thou altogether.

This explains a peculiarity of traditional Quaker speech, which one often hears in films set in the early Americas. The Quakers opposed making any distinctions of rank, so they insisted on addressing everyone as thou, not as you. The irony is that today we perceive thou to be archaic and formal, while the original intent is to be more informal.

Update: we don't know if there was any politeness distinction in PIE. In any case, the distinctions that exist in the modern European languages are not inherited from PIE, since the oldest recorded IE languages (Latin, Greek, Sanskrit) did not have separate polite pronouns. The current European system apparently began with the late Roman Emperors and became widespread in the Middle Ages.

Non-IE languages often have more than two levels of distinctness. In Thai and Japanese (the only two languages about which I can speak with confidence), there are a variety of different pronouns that can be used depending on the exact nature of the social relations between the interlocutors, and the system often extends not just to the 2nd person pronoun but to the 1st and 3rd person pronouns as well.