You need to add it in your themes 'page.xml', which should be here;
MAGE ROOT /app/design/frontend/XXX/YYY/layout/page.xml
Where XXX/YYY are the path to your theme.
Within this file, find this block;
<block type="page/html_head" name="head" as="head">
And add your css like this;
<action method="addCss"><stylesheet>css/custom.css</stylesheet></action>
Refresh your cache afterwards - including the css/js cache if you have merge enabled.
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