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Edit: didn't see jedinite's first post before making this one, oops
Wikipedia rules (http://en.wikipedia.org/wiki/Pwn)
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Other theories of origination
<ul type="square"> A widely accepted origin of the term traces back to the misspelling of the phrase "owned" by a top (or highly skilled) player of the game Quake. The term quickly spread to less significant players; eventually expanding to virtually the entire population of online gamers.
One story reports that in an RTS game (either WarCraft II or StarCraft), someone made a custom map where losing players would see a special message. However, instead of typing in "YOU WERE OWNED," a typo resulted in "YOU WERE PWNED." It is said that every use of the word pwn therefore comes from this one hapless misspelling, or a similar one occurring in another game. This theory is most prevalent.
One explanation is that the word's development mirrors the development of names given to popular programming languages. The 'C Programming Language' was given its name as the next letter after an even earlier 'B'. 'C++' was the name given to the next iterative revision of C, an inside programming joke whereby '++' increases the referent (in this case C) by a value of 1. By the same logic [with the letter 'p' acting as a '++'], the word pwn represents own incremented by a value of 1.
Some people believe that the word was originally a contraction of the term power-owned, pure ownage, pistol-owned, perfectly owned, personally owned, ping-owned, player-owned, professionally owned, powerfully owned, or properly owned or the words Pimped and owned combined. These are probably back-formations.
Still another interpretation makes the case that pwned was not an accident, but instead a contraction of the word pawned. This theory is based upon the idea that the person who was defeated was owned, and then pawned off, as an item would be at a pawnshop (see pawnbroker). It can also be a reference to the weakest piece in the game of chess, the pawn.
One of the ideas of its origin comes from the hacker subculture. Password Own meant that a person owned the root password, and thus no one but the password owner could access that machine any longer. Password owning is such a powerful way to lock down a Unix machine that it explains how pwn could have gained popularity in online gaming as a more powerful version of own.
Another theory supports the idea that pwned originated on gaming forums after the word owned was banned. Administrators banned the word to try to keep flame wars down, and as a result, forum users merely changed the spelling to get past any auto-censors in place. (See also article on Pr0n).
An extension of 'owned', the idea being that you cannot pawn something/someone (sell it to a pawnbroker) unless you have already owned it/them. "You didn't just own them dude, you pawned/pwned them". The popular DOTA Allstars custom map for Warcraft III pops up a message saying "A just pawned B's head for C gold" everytime a player kills another player.
There are some who also believe that pwn is actually a 1337 way of typing "I own." The p is simply the 'I' and the 'o' combined into one letter. Hence, "pwned j00" could be directly translated as "I owned you"
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Of all these theories, the most probable origin is hacker subculture. Examples of its use can be traced as far back as 1986 in an early issue (volume 1, issue 7) of the hacker zine Phrack. That would place its usage well before games like Quake or Warcraft were played.
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The best explanations in order are:
hacker subculture
programming joke
all others
although given the spread of jopke and mrono, i suppose the top-player theory has some credibility.