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I always send all my requests to PHP via mod_rewrite and route using PHP. So all my links are absolute, i.e. /about/something.

I usually write my links like so...

<a href="<?php echo BASE; ?>">home</a>

Where BASE generally translates to / or could be different depending on the base URL.

I remember giving <base href="<?php echo BASE; ?>" /> a go before, but I can't remember why I stopped using it (I think it was giving me headaches).

Are there problems with using this element?

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The href of the base element had, in HTML 4.01, to be an absolute URI. See http://www.w3.org/TR/html4/struct/links.html#h-12.4.

Although some browsers are less strict I believe, I don't think all browsers are consistent in this, so <base href="/"> probably won't work cross-browser.

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I always use base href for the same reason; I use mod_rewrite to make the url into a query string and I don't want to use absolute urls all over the place. So I put one base href at the top. Never had any real issues with it.

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Have you tried doing a javascript "location.href" to a relative url in a subfolder, using base href, in IE? Example: if your base href is "site.com" and your javascript onclick is "window.location.href='folder/targetpage.html';return false;" - in IE this won't work properly if you're already in that subfolder. Do you have a workaround for this?
Never noticed this; so obviously don't really have a workaround.
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OpenCart uses it, Magento 1.7+ does not, Drupal 6 does not. I have run into one custom base href implementation in the past and it seems to make maintenance on the project harder, but that's just my opinion.

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