Internal linking seems to be a factor Penguin is using for ranking. A lot of sites, especially in competitive niches, have used sitewide footers internally and externally. The problem seems to stem from sites that use the footer to link to all or many of the other pages for their site. This can lead to hundreds of thousands of internal links, which looks kind of suspicious.
How can we be smarter?
What would the user expect? Now match that. If it looks unnatural, change it.
Which pages are the most competitive? Use your keyword research, and figure out their difficulties. Look at the sites that rank well, and which keywords will be hard to rank for.
Think about taxonomy. What page types do you have on your site, and how are they structured?
Beware of microsite sitewides. You can use your taxonomies here too. You can try to use sidebars for popular products and competitive keywords, and switch them as their competitiveness changes. Pro tip from John – look at your ccTLDs to internally link, maybe through images or what have you.
- Ask yourself, if I were Google, what would I want to see