I would first like you to tell that there are different ways to solve your problems.
It is the easiest way which is find the code in the layout.xml file inside base which you want to remove for eg:if i want to remove the "My tags" then just comment the portion. <customer_account> tagstag/customer/My Tags </customer_account> But you know that we should not modify the base file,so another next simple method that could be performed is 2.Unsetting the link in your template file.For that copy your navigation.phtml file to your theme (Note: the folder structure should be same) from the base\default\template\customer\account\navigation.phtml. which is shown in above answer.
Another tedious task is to rewrite your core module and creating a method "RemoveLinkByName".which is shown here.link here