If you’re still stuck working with a SQL Server 2000 database, there’s no reason why you shouldn’t be using SSMS 2008 R2. There’s lots of great add-ons for it and provides a rich set of features, aside from merging Query Analyzer and Enteprise Manager.
One thing to watch out for, is that if you script out your database objects, while you’re connected to SQL Server 2000, by default, it will script out TSQL that is compatible only with SQL Server 2008. To switch this, there are two ways:
Tools -> Options -> SQL Server Object Explorer -> Scripting
Database -> Tasks -> Generate Scripts