The word fuck first appears in written English is in a famous line in the poem "Flen Flyys". The poem is mangled Latin and English, and the line reads: non sunt in coeli, quia fvccant vvivys of heli, literally "They are not in heaven because they fuck the women/wives of Ely". It's the word fvccant, with the "u" replaced by a "v" and inflected as if it had been a Latin verb. It was directed at a group of friars, and thus the line was encoded in a very simple substitution cipher. Undoubtedly it was in use before this, but simply not written down due to the taboo nature of the word.

This taboo has in fact made tracing the word through history very difficult (the editors of the original Oxford English Dictionary, for instance, wouldn't include it), and as such it's origin is uncertain. But a valuable clue can be found in the fact that it has cognates in a variety of other Germanic languages where the word can mean "to strike". The archaic Swedish focka, for instance, or Dutch fokken. In Latin, the word for fist is pugnus (as seen in the English word pugilist), and one might surmise a connection to fuck there. The reason is Grimm's law, a sound-shift discovered by Jacob Grimm (yes, the fairy tale collector). This sound shift predicts (among other things) that Proto-Indo-European voiceless stops becomes voiceless fricatives in Germanic languages.

A "stop" is a consonant that in order to pronounce it, you have to obstruct the flow of air to build up pressure which then is released explosively. Examples include p, d and k. A stop is "voiced" if you are using your vocal chords to pronounce it. A d is voiced, a p is voiceless (in order to see the difference, put your hand on your throat and pronounce the two words pop and dad. You should feel your throat vibrate much more on dad than pop because you are using your vocal chords).

A "fricative" is a consonant where air let through a narrow channel. s, f and v are examples. v is voiced, f is voiceless.

Thus, Grimm's law predicts that Latin words with the voiceless stop p should be replaced with the voiceless fricative f when they arrive in English. And indeed, that is very often the case. Latin pes is English foot. Latin pater is English father. Latin penna is English feather. Note that English did not necessarily inherit these words from Latin, but that the words do share the same etymological roots.

And so too, maybe, with pugnus ("fist"), becoming a Germanic root fuk- meaning to strike, which later morphs into our familiar fuck. But unfortunately, this is only a tentative hypothesis, and due to the taboo nature of the word, the true lineage of this wonderful little obscenity will perhaps never be fully explained.