I just finished a site on a dev address and it works in every browser except IE6. When you go to the site in IE6 it just shows an error message "Internet Explorer can not open the Internet site. Operation aborted". This includes the sub-pages and even the cms admin.
Using <% base_tag %></base> wont work, as you will be be closing a self closing tag. You could try <base href="$BaseHref" ></base>.
I am not convinced you are solving the source of this issue with this fix however. I am running a lot of Silverstripe sites with the default <base /> tag and have no problems with IE6.
Of course the lowest rungs of hell are reserved for Internet Explorer 6, but its support for self closing tags in HTML seems fairly similar to other browsers. I have found it seems to have absolutely no support for self closing tags in XML. Is it possible you are somehow making IE think you are viewing XML? Maybe an incorrect Doctype or <? xml ?> tag at the begining of your document?