I have two sites on the same server, both domains resolve to the same IP, this is the way my hosting company has it set up. Since the second site is a folder on the root WWW of the first site, it is in theory possible to get to the second site from the first, for example:
siteb.com, which can also be seen at sitea.com/siteb
However, Google does not have it indexed as such.
The first site is a very high profile site, lots of credibility in Google, PR6 (for what that's worth). The second site was a side project, a blog not related to the first site, absolutely no cross-linking between the two sites.
Because it was a side project, I don't maintain the second site very much. It has some good articles on it, but I haven't written a new article in quite a while. People occasionally post relevant comments on it, and I think there is value having it up, but I'm just not focused on it.
Since I don't look at it much, from time to time, I get blog spam on it. Sometimes it builds up quite a bit. It uses Drupal, and I don't know how to set the comment links to nofollow, so the spam links are not nofollowed.
My question is, can the crap on the second site affect the reputation of the first site, since they are on the same server? It seems like it should not, that these sites should be 100% separate in Google's eyes, but I get quite a bit of spam on the second site, and for a small, insignificant site (PR3), the amount of spam seems disproportionate, leading me to believe that the second site is maybe being targeted due to being on the server of a PR6 site.