The problem I see with yaoi and yuri in anime (this is probably not as much an issue with manga, though) is that the two tend to be played a lot for laughs, or have a certain token-ism about it.
When yaoi shows up as a secondary element in animes that are not outright devoted to yaoi, it tends to be through one specific character who acts as a gay stereotype, and this is done to illicit laughs from the audience (often by having a heterosexual male character be flamboyantly hit on by him).
A good fairly recent example of this is Leeron Littner from
Gurren Lagann.
Now, I genuinely like Leeron. He's a pretty well-rounded character in his own right, and is a productive member of Dai-Gurren. But his homosexuality (not sure if it's explicitly confirmed that he's gay, but it's certainly heavily hinted at) is never really taken seriously. Now, sometimes such homosexuality in anime characters is taken a bit more seriously, but when it is, it tends to result in characters like Creed from
Black Cat, and Papillon from
Buso Renkin.
Both of these guys are very flamboyant, borderline insane, major villains. In both cases, they have
somewhat-to-very unhealthy obsessions with the main male protagonist. In comparison, at least Leeron is very well-adjusted.
So, yaoi characters in non-yaoi specific animes tend to either be comedy relief, or insane villains. Combine that with how gay male characters tend to be all alone in their animes (in the sense that there's rarely another gay male character of note in the anime), and you get a situation where actual gay relationships are not really portrayed in a healthy and serious light.
Now, as a straight man, I don't
particularly care about this, but I find it to be a little bit disconcerting. If nothing else, it seems a bit unrealistic for just one character out of a large cast to be a gay male - i.e. wouldn't the gay male in question want to be around other gay males?
As for yuri... again, even though I'm a straight man, I have to agree with Synaesthetic.
It would be nice to see a yuri relationship played straight for a change (pun intended
).
In other words, it would be nice to see a lesbian relationship portrayed in a more realistic and solidly developed manner, and not merely played for laughs or mildly hinted at. I'm thinking of maybe the lesbian equivalent of one of the two main heterosexual relationships in
Kimi ga Nozomu Eien.