I've searched around for a clean solution for this and I kept on finding articles advising to just comment out the lines in the XML files. This is not ideal as I personally like to make my XML changes in a local.xml file. So here's how I removed the standard footer links in Magento using just my local.xml file.
<default> <reference name="footer_links"> <action method="removeLinkByUrl"><url helper="catalog/map/getCategoryUrl" /></action> <action method="removeLinkByUrl"><url helper="catalogsearch/getSearchTermUrl" /></action> <action method="removeLinkByUrl"><url helper="catalogsearch/getAdvancedSearchUrl" /></action> <action method="removeLinkBlock"><blockname>return_link</blockname></action> </reference> </default>
The only link that I could not remove this way was the Contact link. You can use the above method by removing the link by URL but as I simply wanted to move it to another location this was not suitable. For now I have duplicated my contact.xml file and made the changes in there. If you have a better way then do let me know.