If you ever wanted to remove or change top links (i.e My Cart | My Wishlist | My Account) on Magento you will need to edit several files and here is the list. I would recommend you copy the file to your custom design theme and perform your changes there.
/app/design/frontend/base/default/layout/customer.xml
/app/design/frontend/base/default/layout/wishlist.xml
/app/design/frontend/base/default/layout/checkout.xml
