cr1t1calh1t - 2:29 pm on Feb 1, 2012 (gmt 0)
@robdob - it sounds like you found the smoking gun - the site-wide footer links you placed to your sites.
whether this is a manual penalty or the algo doing its thing - someone else would have to chime in on that. Since it seems like you can point directly to the cause (site-wide footer links), you may want to consider a reconsideration request. Here again, someone else might have better insight on how to proceed.
Google has always been strictly against 'link schemes', but since their definition of a 'link scheme' is quite nebulous, and has probably changed over the years - I have always refrained from linking my sites together unless they are very closely related, and definitely would not do a site-wide footer link.
This is only my own approach, and I can't point to sources to back it up, but I think I've read enough about the inter-linking of sites over the years that avoiding doing so is just second nature to me... I guess I'm just paranoid - the last thing I want is to be considered to be part of a 'link scheme' by Google - either now, or by what their definition of a 'link scheme' might change to in the future.
The thing is, you see tons of sites doing it - but they are generally big brands/media networks, have high traffic, are older, and have more domain authority to where I guess they can get away with it.