sorry to bother...
I'm wondering if anyone could send me a brief list/explanation of bad
things done in the name of shintoism.  (yes, it's for a fic)

I make no claim to be an expert or anything but I don't think there 
is really anything. People, feel free to contradict me....

Shinto revolves around veneration of spirits (both of ancestors and 
things around them) I don't think that it has ever been a rallying 
point for a religious war or anything. Unlike western religions as 
far as I can tell it was never really a centrally organised religion.

This is half-true, IIRC.  (Note:  I'm using what I remember of Mikiso Hane's two
books on Japanese history; I'm certainly expert). 

Shinto and buddhism have competed for power essentially since buddhism first 
came into Japan.  (Confucianism is in there as well, but it tnded to be co-opted
rather than to compete with the other two.)  As far as I can tell, this is 
loosely related to the power of the emperor at any given point; since he's the 
center of the Shinto religion, movements to restore him to power tend to favor 
shinto (e.g. the Meiji era), while the Tokugawa shogunate, for example, favored 
buddhism.  Also, since shinto is native, not imported, it tended to be rallying 
point for nationalism, and so a lot of its most enthusiastic supporters were the
same people who supported, e.g., the abortive invasion of Korea.

To cut a long story short, whenever you have groups vying for power, people 
sometimes do nasty things.  The shintoists have tried to suppress buddhism, 
although never to the extent of, say, massacring them.

Also, the whole concept of "unclean people" (eta) is shinto.  There are several 
categories of people who are in a position equivalent to the outcastes of Indian
society--considered unclean, and forbidden to mingle with them.  Some of these 
categories were hereditary, others not.  Their treatment was pretty rotten, 
although I don't know if it fits into your fanfic or not. 

Gavin