Yesterday, Google announced they have immensely improved the linkage data from Google Webmaster Tools "links to your site" export option for "download sample links."
Previously, the download sample links report downloaded a sampling of links in alphabetical order and stopped after a maximum of 100,001 links. Now, the sampling of links is not done in alphabetical order, instead it is ordered in alphabetical order but rather it is "now sampled uniformly from the full spectrum of backlinks," said Google.
Google said you are now more likely to get "example links from different top-level domains (TLDs) as well as from different domain names," and yes, they will sort them alphabetically for you.
Google said this will make the linkage data "much broader, more diverse cross-section of links."
Why did Google do this? Google said because of the "feedback from the webmaster community." Specifically, Google told us links within the download is enough and then told us it is not enough and then had issues with natural links being marked as unnatural.
I believe this change will make the link reports ALL you need for analyzing your links if you have a penalty.
Google did not confirm that, but they did say they will provide "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."
Forum discussion at Google+.