Planet13 - 7:54 pm on Jun 29, 2013 (gmt 0)
Well, don't know if this will help you decide, but I just submitted a disavow file and I really only included sites that:
1) Had a blog comment from us, or
2) Had a forum profile page from us, or
3) Was a directory with a link to us, or
4) was a link exchange partner, or
5) was a scrape of one of the above sites.
I also tried to remove links from those sites, and even where I WAS able to remove the link, I still disavowed the link.
I didn't bother with all the sites that scrape google results, nor the ones that scrape wikipedia (since wikipedia links to us several times) nor the ones that scrape suite101, squidoo, ehow, chacha, and all the other sites that link to us (since we never used any article marketing on those sites to link to us - it was just the authors of those pages, whoever they were, who acknowledged us as a reference).
"To be honest, I am now completely confused about when its appropriate to use the disavowal tool other than 1) dealing with negative SEO and 2) reversing you own spam links."
I think now it is probably best to focus on #2. Remove as many of those links as you can, disavow them as well even after they are removed, and file a reconsideration request EVEN IF YOU DON'T HAVE A MANUAL PENALTY and just a Penguin problem.