Well, I am joking. “Yes” means “Yes” here, too, most of the time.
However, if you dive deeper into the Japanese web, you may get totally lost in the conversations because of new expressions that continue to emerge.
One phrase which has become very popular since early 2008, is this:
“(subject) desune, wakarimasu.” (～ですね、わかります)
“You said (subject), I totally understand.”
You use it like this:
A: The random killings in Akihabara was terrible news. They must have been caused by the liberal education system introduced by the Americans after the war.
B: You said we should remember the good old days and return to the education methods used in the pre-war era to instill discipline in Japanese youth, I totally understand.
In this example, B is not really agreeing, but not everyone can read between the lines. Person A might even be pleased with B’s response. The deeper you are in Japan’s web culture, the clearer you see that B is trying to make fun of A by using this expression.
Subtle resistance has a long history in Japan. In the era of the Tokugawa Shogunate (during the Edo period), short poems called Senryu (川柳) were written which were like Haiku, but with fewer rules. (For example, in Senryu the writer did not have to include season-related words.) Many of them were sarcastic and included hidden meanings criticizing bureaucrats, the government, and shogun, without explicitly saying so. Jokes made by oppressed Russians under the Soviet regime may have been similar, but the Japanese at that time preferred more crooked jokes with double-meanings.
Japanese people generally tend to avoid confrontation, which makes the majority of them think that discussions, negotiations and quarrels are all just “disputes” and bad for society (which is the main reason I think social news/discussion sites like Slashdot Japan and Digg clones are not popular in the Japanese web community). Showing one’s disagreement with wit instead of straightforward counterargument is welcomed more by readers. I think this is one reason why this expression’s popularity exploded so quickly in 2008.