1573, "resembling skin," from skin (n.). Meaning "emaciated" is recorded from 1605. In the sense of "the truth" it is World War II military slang, perhaps from the notion of the "naked" truth. Skinny-dip first recorded 1950s.
1869, from scrag "a raw-bones; a skinny person" (1542), probably from a Scand. source (cf. Norw. skragg "a lean person," dialectal Swed. skragge "old and torn thing," Dan. skrog "hull, carcass"); perhaps related to shrink (q.v.). Scraggy "gaunt and wasted" is attested from 1611.
1661, "kind of tights" (originally a Fr. fashion and execrated as such by late 17c. Eng. writers), associated with Pantaloun (1590), silly old man character in It. comedy who wore tight trousers over his skinny legs, from It. Pantalone, originally San Pantaleone, Christian martyr, a popular saint in Venice (Pantaleone in the comedies represents the Venetian). The name is of Gk. origin and means "all-compassionate." Applied to tight long trousers (replacing knee-breeches) by 1798; pants is a shortened form first recorded 1840.