[Problem]
After installing a MS Server 2003 OS and applying the SP, and then installing SQL 2000 and applying the servicepack 3a (SQL 2000 does not work on W2003Server without this servicepack!), we had problems connecting enterprise managers and applications (BDE, ..) to the newly created server.
[Solution]
After making sure that there was no security policies problem, i slammend by head on the desk, and deinstalled SQL. Then, at reinstall, i chose the custom mode and went through the installation again. You will be asked once in a tiny window if you want a "default" installation or a different type - chose default there, because the other type will install the SQL 2000 Server as an Oracle-style instance. However, the SP3a seems to switch the mode to instanced per default, too, so make sure you dont run this type when having problems connecting with applications.
After the server was not Instanced anymore (so SERVERNAME instead of SERVERNAME\INSTANCE or SERVERNAME$INSTANCE), we could easily connect with all our apps again!