Google pushed out Penguin 2.0 a couple of days ago, on the 22nd, and Matt Cutts had been trailing it for weeks as a bigger change than the earlier refreshes. Having had a look at the early chatter and a few sites I keep an eye on, I think he was right. This one goes further than the first Penguin did, and a fair few people are going to feel it.
The headline difference, as I understand it, is depth. The original Penguin last spring largely looked at links pointing to your homepage and top-level pages. This version reaches further into the site, examining the links to your deeper pages too. If someone had been building dodgy links to internal category or product pages on the assumption that Penguin only cared about the front door, that assumption has just stopped working.
That matters for a specific kind of site. Anyone who spread their link building around, pointing spammy anchors at inner pages to avoid concentrating risk on the homepage, has effectively been caught by the update closing that gap.
If you are worried, here is roughly the order I would work through things.
First, pull your full link profile. Webmaster Tools gives you a download of the links Google knows about, and that is the right place to start because it is Google’s own view rather than a third party’s approximation. Look at it with a cold eye. You are hunting for the links you would be embarrassed to explain to a client: site-wide footer links, obvious paid placements with commercial anchor text, links from networks that exist purely to sell links, comment and forum spam with your keywords in it.
Second, look at your anchor text distribution across the whole site rather than just the homepage. A natural profile is mostly your brand name, your URL, and generic phrases like “click here” or “read more”. A profile that is heavy on exact-match commercial phrases stands out, and now it stands out on your inner pages as well as your front page.
Third, if you find genuinely bad links, the sensible path is to try to get them removed at source, keep a record of that effort, and use the disavow tool for whatever you cannot shift. Google introduced disavow precisely for this situation, and after an update like this it is going to get plenty of use.
I would resist the urge to panic and rip out everything that is not perfect. Some ordinary, slightly untidy links are part of any real profile and pulling them out helps nobody.
For anyone who has always earned links the slow, proper way, this week is a non-event and possibly a small gift, since some of the competitors who were gaming it may have just dropped away. For everyone else, the work starts with that link export, so I would go and download it.