ZydoSEO - 1:43 pm on Feb 4, 2013 (gmt 0)
I don't think Uli was saying to "only" use WMT. But it's a great place to start IMO. These are links that Google definitely knows about and therefore could be affecting your rankings. And it's something that every webmaster has at their disposal for free.
Of course, if you have access to other paid tools like Majestic, OSE, etc. then by all means you should supplement the WMT list with data from those sources as well. But links shown in Majestic, OSE, and other tools that crawl the web independently might not be included in Google's link graph and might have zero affect on your rankings at the moment (though they could in the future).
For most sites, WMT gives you a decent sample of linking domains on the "Who links the most" page plus it tells you the number of links they know about from that domain ("Links") and how many different URLs on your site they are linking to ("Linked pages"). By sorting the WMT list by "Links" descending, sites linking to your site using site wide links (blogrolls, footer links, etc.) are easily identified since they float to the top of the list.
A quick visit to the home page of each of those domains with multiple links to your site is typically all it takes to find and evaluate the links. If you're selling DVDs online and your site's link is in a blogroll next to links for "Online Poker", "Hot Asian Girls", etc. then that is not the kind of link placement you want to keep (regardless of whether you paid for it, your competitor did to set you up, or it was a natural link). If you can't get such links taken down then they are candidates for the disavow tool. Specifically, these are candidates where you might want to use the domain: directive since you don't want to have to identify and disavow possibly hundreds or thousands of URLs from a single linking site.