Yaoi is the Japanese term for male-to male sexual relations. However, as with all things Japanese, there's usually a pattern.
There is the uke, or female-designated partner, who is usually prettier (although sometimes not by much), smaller, and needs to be protected all the time as he is constantly wandering off and getting raped, kidnapped, seduced by other men, heartbroken, etc. The word uke comes from the Japanese for "receptacle".
The male-designated partner is called the seme. He usually leads the relationship, often to the point of practically forcing himself on the uke, but he is very protective. Seme is from the Japanese word semeru, meaning "to attack".
Yaoi is also short for yama-nashi, ochi-nashi, imi-nashi, which basically means "no climax, no point, no meaning". Basically the only reason to write stories like this was to get two lovely boys in bed together as fast as possible.
Since then, however, yaoi seems to have changed a bit, especially with the advent of the non-Japanese fan fiction writers. Yaoi in Japan has also modernized somewhat, but is still fairly predictable in terms of who will end up with whom in the end. Also, yaoi manga and anime still consist mostly of sex and angst (beautifully drawn, of course), while sketching out the bare bones of a plot.
The genre of yaoi fan fiction, however, is very different. Sex goes side by side with, or even takes a back seat to, story. Except of course as in the case of the plot-what-plots. There are tons of amazing writers exploring the strange and lovely world of yaoi.
This is not to say, however, that yaoi manga should be considered inferior. On the contrary, it is the backbone and the inspiration of these wonderful writers. Fan fiction, no matter how brilliant, is still after all fan fiction. And even the original stories rise out of the inspiration of the Japanese stories and gorgeous artwork.
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