"If I download my backlinks in Webmaster Tools, my list ends at H. If you are Amazon or eBay, you get 000000a.com to 000000c.com," Cutts said.
When Google is serving 100,000 backlinks in Webmaster Tools, it wasn't that useful to users when they could get so many results from a single domain, and there was no way to sort them.
Shortly after the announcement this morning at SES, Google published a blog post detailing the changes:
Based on feedback from the webmaster community, we're improving how we select these backlinks to give sites a fuller picture of their backlink profile. The most significant improvement you'll see is that most of the links are now sampled uniformly from the full spectrum of backlinks rather than alphabetically. You're also more likely to get example links from different top-level domains (TLDs) as well as from different domain names. The new links you see will still be sorted alphabetically.This is a great change for webmasters, especially when people are trying to clean up after receiving a bad backlink warning. This was a problem for larger sites, and especially if someone was cleaning up a site that had thousands of low-quality/spammy backlinks pointing to a site.
Starting soon, when you download your data, you'll notice a much broader, more diverse cross-section of links. Site owners looking for insights into who recommends their content will now have a better overview of those links, and those working on cleaning up any bad linking practices will find it easier to see where to spend their time and effort.
The change has already gone live, so you can download a better cross-section of your backlinks in Google Webmaster Central right now.