Now that Google has withdrawn our ability to see the inbound links to our sites, alternative discovery techniques need to be investigated.
In case you have not been reading this site, Google used to show us all the links pointing to our sites. Just prior to 1 July 2010, they restricted the available metrics to only a small "sample" set of links. For some of our clients, this sample is less than 0.1% of their total links. A very deceptive link labeled "Download all external links" still sits at the bottom of the inbound links list, but this will only get you the sample list, not all external links.
Go take a look and see how your site is handled. Most large commerce sites will have pretty big numbers - 100,000 links is very common. If you have those kinds of numbers, then you're probably going to be disappointed to see the size of the 'sample' available to you in WMT.
We're working on alternatives, but really there are none that will tell us what Google is crediting our sites with. Many external tools, like seomoz, Yahoo linkdomain searches, etc. will show you a set of inbound links, so getting a list is not the problem. The issue is that if you're trying to run forensics on a rank problem in Google, you want to discover what Google is crediting you with, not all the links pointing at your site. This is especially important since Google never indexes or credits ALL the links, so being able to see the specific sources is what matters.
My question to Webmaster Central within Google forums has not been answered: Is the removal of inbound link metrics from WMT a permanent degradation of that tool? This leads me to suspect it's gone for good and that so few people care that there will be no pushback.
More on coping later.