Using Webmaster I can see the home page of a related site has 100,000 + links to my site. I assume this is because there are tons of pages on this site and a link to our site is in the footer.My question is how does Google treat this? Surely this must be quite common for huge sites, but does Google see this as suspicious? Do they rank each link or consider the site as a whole and only rank a single link?
What are the implications of one site having thousands of links to yours?
links;pagerank
It is not that suspicious alone.    I own a currency conversion website that commonly gets links on every page of sites that use it to convert prices. When site-wide links are combined with other spam indicators, then it could become a problem. keyword rich anchor texthidden texton low quality pages among other links that are clearly bought