Hmm.. stil not sure what the BASE HREF is good for, never used it before I entered the oscommerce world, but it might be there for a good reason.
You can also work around this problem by using this:
<a href="<?php echo $_SERVER['REQUEST_URI']; ?>#top">Top</a>
Works like a normal anchor tag (so without reloading the whole page), the session is retained, and you can keep the BASE HREF.
@Jeremy: using the tep_href the whole page is reloaded after every click, or isn't it?
@Amanda: You remind me, I have got to work on my languages switch :D