That’s a HE!! of a good question! The serious answer is an “I don’t know for sure”. I don’t think it’s documented except as listed above in the wikipedia answer for pop culture. But as far as its usage, I’m sure it pre-dates the response. I explored that many years back with a sub in conversation and naturally it came down to an authority, Dominance and control situation where she had been molested by her dad, but felt it was “safe” to role play it in her adult years, and was even comforted by it in some strange way. As a man, it’s definitely a control thing. It used to bother me when I’d say it in a sexual situation, because of the natural reasons, until I figured out that it wasn’t the actual Daddy/daughter thing… because that is repugnant in it’s drawn out conclusions. Finally, I just let it go, chalking it up to Control. So in that sense, I have no doubt that it was started out in the BDSM scene by those with baby-girl, daddydom issues, and then translated over into the pop culture side as a joke which caught on, and became “safe” to use.

On the funny side – well – I don’t even have a quick response to it… lol.

Although the copied and pasted answer above seems plausible, don’t fall for that internet claptrap. It is, in a word, nonsense. The phrase was in use in trailer parks long before 1968. The special bonding prevalent in those wheeled plywood and aluminum abodes gave rise to the phrase. Etymologists disagree, but they theorize that it evolved from the root phrase, “I’m the daddy,” meaning I’m in charge and you’ll do as I say. It was thought to be uttered along with, “You’d better not tell your mother,” and “Nobody’s ever gonna believe your skinny @ss.” As the late night pillow talk progressed and the males needed reassurance regarding their prowess, the phrase morphed into the familiar, “Who’s your daddy?” Not to be confused with the world weary fourteen year old girl’s refrain, “Get off me Daddy, you’re crushing my smokes.” The homosexual equivalent of the phrase was popularized on the television program Gilligan’s Island. The progressive show featured the lovers Captain and Gilligan, and you could be sure that the randy Captain was about to get off whenever he winked and exclaimed, “Hey there, little buddy.”

The phrase itself stands out as a noteworthy lyric from the 1968 song Time of the Season by The Zombies: “What’s your name? Who’s your daddy? Is he rich like me?”

Widespread provocative use of the phrase began as early as the late 1980’s, [1] largely due to its frequent use in sexually suggestive skits broadcast by a popular syndicated radio shock jock known as “The Greaseman”.

A particular catalyst for widespread use of the phrase was the 1990 film Kindergarten Cop [1]. In the film, the line “Who is my daddy?” [2] was spoken by an Austrian actor(a modern masculine archetype) Arnold Schwarzenegger. The clip was promptly audio sampled by The Greaseman, the Jerky Boys, and others, for use in humorous, typically homoerotic radio skits. The expression was further popularized in a well known 1991 comedy routine by Dennis Miller; additionally, then-host Craig Kilborn used the phrase “Who’s your daddy — is he rich like me?” on an early episode of The Daily Show.

In the 2004 American League Championship Series it was used as a mocking chant by New York Yankees fans against Boston Red Sox pitcher Pedro Martinez (prompted by his previous statement, “I… call the Yankees my daddy” [3]). It was so popular that T-shirts were made referencing it. The Red Sox went on to win the series 4-3 after being down 3 games to 0, as many Red Sox fans began using the chant against Yankees fans, spawning retaliatory T-shirts of their own that had the phrase “Whose your Papi?” referring to David Ortiz since he was so clutch in Game 4 and 5 of the series getting 2 walk-off hits.

One variant commonly targeted at residents of Indiana is “Hoosier Daddy?” [4]

Joseph Massino is also known for his famous line ‘Quien es tu papa?’

http://en.wikipedia.org/wiki/Who%27s_your_daddy%3F_%28phrase%29