Shounen:
Consisting of stories geared toward boys, Shounen show characters overcoming challenges. They also contain everyday, comedy/parody or drama situations, but do not contain overt sexual situations.
 

Shoujo Ai:
Shoujo is a class of stories aimed at female audiences. However "Ai" means "love" in Japanese, indicating that this is a tale about love between women. These contain homosexual (female-female) couplings in them.
The sexual scenes are very romantic in nature and do not usually show explicit details.
 

Shounen Ai:
Similar to the Shoujo Ai class, Shoujo Ai features love stories between two men.
The sexual scenes are typically very romantic in nature and do not usually show explicit details. The focal plot element is love.
 

Yuri:
Unlike Shoujo Ai, Yuri stories are characterized with women engaging in relationships more sexual than romantic. It got it's name from having so many of the characters having the name of "Yuri," meaning lily.
 

Yaoi:
Yaoi is an acronym for 'yama nashi, ochi nashi, imi nashi': no climax, no point, no meaning. These stories feature sexual male couplings with very little romance. The plot revolves around pleasurable sex.
 

Lemon:
This term is usually used to describe a story with lots of sex with very little romance involved. "Having a bitter-sweet romance" was a phrase coined in England in the 1830's to describe couples engaging in wanton sex. Since lemons give off a "bitter-sweet" flavor when tasted, this metaphor was used to insinuate people going about such "scandalous" behavior during that time.
Though this term is also widly used to describe stories containing sex.
 

Lime:
Unlike Lemon, this is only hinted sex.
 

Seme and Uke:
These stand for the Japanese sexual configuration: the passive person is the uke. The active person is the seme.

Seme = top: from the verb 'semeru', attack
Uke = bottom: from the verb 'ukeru', receive

In Japanese comic books, convention is to put the seme/top's name first. Yuri/Yaoi uses the 'x' to separate partners rather than the western "/".
 

The Height Rule:
The tendency of fans to decide which character in a series is the seme on the basis of which is the taller.
The reason behind the height rule is probably the visual nature of yuri/yaoi: a short top looks funny to many people, just as the shorter man/taller woman configuration still strikes some people as odd.