This question seems to be coming up a lot lately so I figured that I would make this post to try and help settle the issue some. While the evaluation version of Configuration Manager 2007 is fully functional--for 120 days at least :), SMS 2003 has never supported upgrades to, or from, evaluation code to fully licensed code. In other words, you cannot upgrade an SMS 2003 site using the evaluation version of Configuration Manager 2007 and you can't upgrade an SMS 2003 trial software installation with Configuration Manager 2007.
The blocking of upgrading to an evaluation version (and vice-versa) is a function of the SMS 2003 code and is not the case with Configuration Manager installations. If you have an existing installation of the evaluation version software of Configuration Manager 2007, you can upgrade to the full version of Configuration Manager 2007 as long as you do it before the 120 day evaluation period has expired.
I hope this helps,
~Jeff
P.S. To get the 120 day evaluation version of Configuration Manager, go to: http://www.microsoft.com/downloads/details.aspx?FamilyID=23945ee2-bd1e-4bd8-a5fa-3e846fd8bd49&DisplayLang=en