We just recived (March 8 2013) a message from Google saying.
We've detected that some of your site's pages may be using techniques that are outside Google's Webmaster Guidelines. Specifically, look for possibly artificial or unnatural links pointing to your site that could be intended to manipulate PageRank. Examples of unnatural linking could include buying links to pass PageRank or participating in link schemes. We encourage you to make changes to your site so that it meets our quality guidelines. Once you've made these changes, please submit your site for reconsideration in Google's search results.
Our site is AlternativeTo and it's a big well respected software site and we have never ever bought any links or anything like that. We recive natural links from places like BBC, Reddit, Lifehacker, cnet and so on.
Anyway we do however have some sites that is using our API and are sending 100.000+ links back to us from their domains and i also see some other rather dodgy looking sites with low page rank linking to us. Nothing that i can clearly say are spam but well they look bad and have lots of ads on them.
How the heck would i know what links to remove? I mean we have hundredthousands backlinks from all over the web to our site. Where to start?
I found Matt Cutts suggestions about downloading recent links and so on but there are still hundreds of new links discovered by google each day ..
Anyone have any suggestions about this? Should i ask the sites that are using our API to put no-follow on their links to us to avoid these 100.000+ links from single domain names?