Which backlinks to disavow?

How do you decide?

[Broadway]

I've been checking my website's backlinks via webmaster tools.
I've found a few sites where they've chosen to use my website as one of their "authority" links in either their footer an index.
Sometimes, the other authority sites in the same list of links are prominent .org's or other decent .com's.
These links are usually part of the website's standard page format, so maybe 20 to 100 links come from that website to (usually) just 1 or 2 pages on my site.

The fact that the linking comes from a footer or an index creates an unnatural appearance, in the sense that it's not in-text linking.
Some of these sites doing the linking have a Google website pagerank of 2 up to 4. So, while they seem kind of spammy, they're not entirely so in Google's eyes.

I would think these are exactly the types of links that websites would like to buy. However, I wouldn't think the .org's did. And I certainly didn't. And if links were being sold, you would think they could have sold the space they use for links to my site.
(I guess someone could have sabotaged me by buying links for my site, but there's no real reason to expect that that happened.)

I'd want these links in a second if it wasn't for the fact that there are just so many of them.

But because of their number, they give an impression of being unnatural but I'm hesitant to rock the boat by Disavowing them or requesting them to be removed or nofollowed due to the pagerank of the websites.

Anyone have any advice as to how they decide which websites to disassociate from when it's not a situation where
they bought or arranged for the links?

[n0tSEO]

My suggestion would be to contact the webmaster and ask if they placed the links editorially or if someone sold them to them. If the latter is the case, check with them and ask for removal; if it's the former case (editorial links), ask them to move the links to an in-text context, so they are no longer in the footer (or to keep them in the footer with a rel=nofollow attribute, if they wish).

[martinibuster]

Are you pro-actively disavowing links? If you have engaged in questionable linking schemes, including asking for specific anchor text, then it's probably a good idea to ask for those links to be removed or no-followed and requested keyword optimized anchor text branded, even if no-followed.

But if you haven't done anything at all then you're probably ok. Most high ranking sites attract low quality links.

[vandelayweb]

As long as you didn't purchase these links or you didn't hire an SEO firm who may have done this on your behalf, I wouldn't worry about these links. Its basically a vote of confidence from that site to yours as natural linking should be. If you are an authoritative site, then there is no reason anyone would question that sitewide link placement. People see value in your content.

With that said, I'd also look at those other sitewide links to judge their value. Are they also high value sites that make sense that the site owner would want to highlight? If you were nested within a bunch of trashy links, then it would be prudent to disavow so you aren't guilty be association.

As far as proactive disavowing goes, I'd only target the links that don't look natural and don't add overall value. Try to remove yourself from the situation and view those links like a Google webspam team member might.