I have seen two entries on this today that need flagging.  The 1st is the re-iteration by Susan Bradley that everything works baring e-mail in a WSS v3 site - providing you are not upgrading a WSSv2 site on SBS.  Side-by-side installs work with this exception.  It is still vital that you read this document before you do the upgrade.

However, I have had several people mail me asking how to recover.  I asked the same question inside Microsoft and was told that a potential solution has been documented in a blog - http://blogs.technet.com/edwalt/archive/2006/11/29/removing-wss-3-0-companyweb-upgrade-restoring-wss-2-0-on-sbs-2003.aspx.  This is almost certainly great news for those who ruin their site.  There is a word of warning - you need a backup of your WSS v3 companyweb database.

ttfn

David