Today I was working on a mobile theme for a client of ours and I needed to remove the printer friendly link from every page. The first thing I did was create a hook_link_alter() function in my custom module and quickly realized this would alter every theme.
I came across this article (http://drupal.org/node/46961) that lead me to the
$theme_key variable. Using this I quickly limited my hook_link_alter function to the proper theme.