Ekul wrote...
This is actually a fairly complicated legal question, but in general, no, they do not.
A doujinshi is an unlicensed derivative work. As such, its creator is generally not entitled to copyright protection, since they do not own the copyright they are attempting to enforce. If they created a new character they could claim copyright on that, or if they created a distinct enough plotline, they could perhaps claim that. But even that is questionable, since the entire thing is an unlicensed derivative and as such the entire thing makes the author liable to the original creator for infringement.
The whole legal issue behind doujinshi is pretty interesting and complex. There have even been a few thesis papers written on the subject. Even the late Yoshihiro Yonezawa published a book that basically outlines tons of suggestions on how to deal with the doujinshi situation:
http://www.amazon.com/gp/product/4883790894
Within Japan, there is technically no fair-use clause in their copyright law. Because of this, those who make jokes, parodies, or criticisms of a trademarked or copyrighted material can be sued by the original copyright holders. However, the amount of lawsuits within Japan over copyright issues is pretty low compared to the US. It's something like in the 100 - 300 cases a year range according the the Japanese Supreme Court.
So, exactly why have Doujinshi been allowed? Well there are a number of factors for this reason. One of the biggest one however is the fact that the works are technically only sold on a single day and in very limited quantities. Comiket is a three day event, however, it is broken up into different categories per day. "Family", "Women", and "Fetish". Artist will book a table during the day that most relates to their work and be there for that single day only. They will sell their doujinshi for something like 500 ~ 800 yen and then the rest of the stock will be bought up by Toranoana and other third party stores who will resell it.
Wonder Festival is a similar situation to comiket. There is a fan area, where amateur sculptors sell garage kits of their fan made figures in limited quantities to attendees. How do they get away with this? Well, within the industry they basically grant all sellers within a fan section a "limited license" which allows them to sell the kit for only that day.
Both Comiket and Wonder Festival's organizations tend to look through what will be being sold for those days. If anything seems to be a bad idea (if a particular company is super against doujinshi/parody works) they will work with the artist/seller to see if they can come to some solution.
That's not to say that the doujinshi world hasn't had it's share of legal issues in the past. Back in 1999, Nintendo went after an artist for a Pokemon parody doujinshi she self published. This issue was HUGE. So much as that it's what basically began the huge talks of the legality of Doujinshi.
It's honestly all very complex and all kinds of crazy. A lot of the law is vague and companies don't really want to get into lawsuits over it.
One really good thesis paper I came across before was Nele Noppe's
"The cultural economy of fanwork in Japan". Despite what some may think of it, it does contain a lot of really good cited information on how the entire doujinshi process happens from start to end. It even touches on the reason why doujinshi artists put the disclaimers in the back against auctions.