I don't like the idea of the disavow file (which I will not get into here) so I have resisted creating one for my 11 year old site.
I have never gotten a manual penalty and I have never participated in blackhat techniques.
With the latest Penguin though I can't afford not to create one with the hopes it will help.
I have about 30,000 links to wade through and after going through a couple of hundred I have a few questions.
1) Well adding the domain line to the file
domain:example.com
block all sub domains as well?
2) According to Google I have a lot of spam sites pointing to me that when I visit them don't actually have a link to my domain. Is it best practise to block these anyways incase the site is randomly adding links to their pages or other underhanded techniques?
3) For those of you who have recovered to a degree from Penguin and you believe your disavow file helped, how stringent were you with disavowing a domain/link? I have a number of links that I would consider being from a spam site but then I notice that Google has given then a page rank of 2 or higher. I haven't bothered with page rank for a while but you have to wonder why some of these sites rank?
My plan is to disavow the most obvious spam backlinks with the hopes that Google will run Penguin again fairly soon (like they said they plan to do). If I don't see any returns I would then add ones that I am not sure about.