While you probably won't be penalized for having duplicate navigational links in the footer, I am not sure that makes any sense to have them (if they are just duplicating the main navigation).
I don't know what the exact effect will be on page rank, but it COULD have a negative effect on the ability to flow page rank to other pages.
Zappos has something similar...
And Zappos probably has hundreds of thousands of inbound links from external sites, so what they can get away with when distributing page rank is probably a lot different from what you can get away with.
Unless you have that massive amount of Page Rank equity that Zappos has, it would be best to find a better suited way of setting up internal links, and I would suggest that better way would NOT be duplicating navigational links.
Similarly, many people have tried to replicate the way that wikipedia links internally, with dozens, if not hundreds, of internal links on a single long page. The reports I have heard is that they almost invariably lead to POORER rankings.
I hope this helps. To be honest, this is really a question for the google thread instead of the link development thread. You would probably get more lively debate if it were moved to that thread.