You would use the method explicitly if you are working with Web Pages 1 and want to ensure that your virtual paths always map correctly to an absolute url. From Web Pages 2, the Href method is called by the framework if the parser encounters a tilde (~) in a url in your cshtml file e.g.
<script type="text/javascript" src="~/Scripts/jquery.js"></script>
When might a path not resolve correctly without using the Href method explicitly or tilde? It might not work if your site's root path structure changes if you change hosting for example. It also might not work if your internal folder structure changes, or if you move files about. If that is unlikely to happen, you probably don't need to worry about using the method. I didn't tend to use it until the Href method was replaced by the tilde. Now I always use it on the basis that it is so much easier to use, and I would prefer to add one additional keystroke to each url than be sorry at some stage in the future.
You can find out more about Href about half way down this page: http://www.asp.net/web-pages/tutorials/basics/2-introduction-to-asp-net-web-programming-using-the-razor-syntax