"with reference to," used from c. 1700 in legalese, from Latin (in) re "in the matter of," from ablative of res "property, goods; matter, thing, affair," from Proto-Italic *re-, from PIE *reh-i- "wealth, goods" (source also of Sanskrit rayi- "property, goods," Avestan raii-i- "wealth"). Its non-legalese use is execrated by Fowler in three different sections of "Modern English Usage."
1570s, "conclusion or final adjustment and settlement of some matter," from verbal phrase wind up (see wind (v.1)). Baseball pitching sense attested from 1906.
1560s, "act of staining," from stain (v.). Meaning "a stain mark, discoloration produced by foreign matter" is from 1580s. Meaning "dye used in staining" is from 1758.