I have downloaded the latest version (3.5.2) to try it out. On the "Browse for database" screen for SQL Server, when I set the connection to a SQL Server 2000 server and press refresh to retrieve the list of databases, I get the following error: Invalid object name 'sysdatabases'. So I checked, and it's still there in "master".
I've worked out what is the problem. I'm using Windows Authentication, and the default database for my account (which is set to System Administrator) is something other than "master". When I switched my default database to "master", the database list refresh worked. The program code obviously does not explicitly look for "sysdatabases" in "master". This needs to be fixed.