System.Web.Mvc
is specific to the MVC framework.
System.Web.WebPages.Html
is for use with Web Pages that use Razor.
To be honest I've never used them in Web Pages but the examples I have seen they look identical, I just remember to never select the WebPages namespace.
There is an example available here:
http://www.mikesdotnetting.com/Article/184/HTML-Helpers-For-Forms-In-Razor-Web-Pages