Mods note: I should mention that I have seen HymnSite's
site. I took only a very brief look at it when I needed to remove the url of the site from an earlier post. Per our Charter and TOS, we can't get into public discussions of the any site... but for the purpose of this thread not going in the wrong direction, I can disclose that there are many technical issues with the site.
Numerous navigation links when I looked at the site were broken and returned 404 error messages. The navigation itself wasn't structured into what I felt might be searchable categories.
The site was built in frames, something I haven't seen in many years, which provide lots of challenges for search engines. Even if Google did index the framed pages, the content frames simply not well optimized, nor was the content focused. As I remember, the page titles were often repetitiive, and there was no way that titles could have been used to boost relevant content.
Additionally, there's what appears to be a great deal of duplicate content on the site... as I remember without any sort of value-added commentary. Again, we can't get into a discussion of site specifics in a public area of the forum.
I bring this up, though, to suggest that the site was probably ranking on inbound links alone, and it's possible that some aspect of the site's inbound linking, or the linking algorithm, changed significantly around Feb 28. Treatment of (or threshold for) duplicate content may have also changed.
The site did appear on the surface to be extremely well linked, but I did not check the backlinks for Penguin purposes at all.
Possibly, there was a high proportion of link exchanges in the backlink profile.
How do you pick domains for your disavow file?
Up in the top left of almost all pages on WebmasterWorld is a free tools
The first tool listed is a backlink checker tool for disavow link analysis that I think will help you... Google Backlink Checker Tool for Penguin & Disavow Analysis http://backlinks.webmasterworld.com/google-backlink-tool-penguin-disavow/
I suggest that you first view the two videos about using the tool on the above page. These tools and the videos have been posted by Jim Boykin, whose company owns WebmasterWorld. The tool is in beta, and is free.
The videos are among the best presentations I've seen about the kinds of patterns to look for in analyzing backlinks for disavow. As the videos suggest, there's no pushbutton way to approach this. The patterns can vary from site to site.
If you did a lot of link exchange, you may need to remove your links to partner sites. Before submitting disavow, I would contact site owners and politely request that links be removed. Keep succinct and careful records on these requests, as you will want to submit them with a subsequent disavow request.
This is only a very partial a summary description of what needs to be done. Definitely disavow by domain... don't try to hang on to some of the links in the hopes that they will do you some good.
I would first fix the many technical problems with the site before disavowing.