Google has always made it hard to see link data. First they made the link: query intentionally vague and then when they showed link data in Webmaster Tools it only showed the first 1000 domains.
This was fine when we all just wanted to see our best links but when Google started to penalise sites for low quality links that they were not showing in Webmaster Tools because they were beyond the 1000 domain limit a lot of webmasters got pretty annoyed. It’s pretty hard to recover from a penalty if you are getting penalised for links that you can’t find anywhere.
How can you remove/disavow links you can’t see? Google, please can you show more than 1000 domains in WMT @mattcutts
— Tim Grice (@Tim_Grice) November 30, 2012
Luckily (assuming this isn’t a bug) Google has finally listened to our pleas and has just started offering us the ability to get way more than 1000 domains. We have had a few instances of 2500+ domains being returned via this method in the past couple of weeks. The interface has not changed and it does still say “1000 domains” but if you click the “Download latest links” button in the Traffic > Links to your site screen then you should see way more than 1000 unique domains. The other buttons still just return 1000.
Keep in mind you just get a raw list of links so you need to extract the domain in Excel, I use the “text to columns” function and split by a forward slash.