Middle English, from Old English eow, dative and accusative plural of þu (see thou) and objective case of ge, "ye" (see ye), from Proto-Germanic *juz-, *iwwiz (source also of Old Norse yor, Old Saxon iu, Old Frisian iuwe, Middle Dutch, Dutch u, Old High German iu, iuwih, German euch), from PIE *yu, second person (plural) pronoun.
The pronunciations of you and the nominative form ye gradually merged from 14c.; the distinction between them passed out of general usage by 1600.
Widespread use of French in England after 12c. gave English you the same association as French vous, and it began to drive out singular nominative thou, first as a sign of respect (similar to the "royal we") when addressing superiors, then equals and strangers, and ultimately (by c. 1575) becoming the general form of address.
You know as a parenthetical filler is from 1712, but it has roots in 14c.; as as a euphemism for a thing or situation unmentionable it is from 1867. You never know as a response to something unexpected is attested from 1924.
Phrase you-know-what in place of something deliberately not named is by c. 1600 (1540s as you wot what). You-know-who (or whom) for a person it is thought best not to name (but implying the hearer knows) is by 1766. You never know as a response to something unexpected is attested from 1924.
Through 13c. English also retained a dual pronoun ink "you two; your two selves; each other."