I had 5 sites suddenly dropped completely out of the Google index July 29, but it's a real mystery trying to figure out if this is because of something I did or just part of the collateral damage. 2 of my sites were also dropped from Yahoo in June, but I don't know if there's any relationship.
Since we're not allowed to post URLs here, I would like to send you a few of mine in a sticky note if that's ok with you so I could ask you to take a quick look at them.
I use a small reciprocal links directory that I have to manually manage, and it does contain it's share of unrelated links, gambling, pills, etc... but the links are subdivided into their own pages, so all related links are on their own page. I also have a few related and unrelated homepage link exchanges. I am using a page generation software "Rankingpower" but nobody, including google seems to have an answer for that.