There are a couple of different .NET XSLT functions that I see used in the out of the box SharePoint web parts (RSS Viewer and Data View web part).
<xsl:stylesheet
xmlns:ddwrt="http://schemas.microsoft.com/WebParts/v2/DataView/runtime"
xmlns:rssaggwrt="http://schemas.microsoft.com/WebParts/v3/rssagg/runtime"
...>
...
<xsl:value-of select="rssaggwrt:MakeSafe($Html)"/>
<a href="{ddwrt:EnsureAllowedProtocol(string(link))}">More...</a>
...
</xsl:stylesheet>
Where can I find a reference that describes all of the extension functions that SharePoint provides?
I have been wanting more info on ddwrt as well. The most information I have been able to find is from Serge van den Oever that was later turned into the MSDN article referenced in the previous answer.
http://weblogs.asp.net/soever/archive/2005/01/03/345535.aspx
As he noted in his blog post, this article contains some info that was censored in the MSDN article.
Other than this article, there is very little written on the topic. It unfortunately appears that scouring existing generated code (such as the xsl in DataForm web parts) is the best technique to learn more at present.