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I'm using joomla sites. I now know how they got into our sites. We had malware on one of the computers, and apparantly keeps filezilla the passwords in a text files without encryption. I have changed all the comprimised files back, and changed every password on the sites. The hack changed every index and footer file. Let's hope it doesn't came back.

Try to keep anchor text links to 30-40% maximum if you want to steer clear of Penguin. The rest of your anchors should be things like your brand name, your URL, "click here", etc. Look at the link profiles of other sites to see what a more natural profile looks like. Ultimately you want to avoid links where you have control over anchor text in the first place, and try to attract organic links to your site, which is ultimately what Google wants.