The next major version of SQL Compare, expected October/November this year, will not support SQL Server 2000.
SQL Compare 11 will remain available to use with SQL Server 2000, although it will not receive any more updates. (Originally SQL Compare 11 wasn't going to support SQL Server 2000, but we reversed the decision after customer feedback.)
After the release of SQL Compare 12, the other tools using the SQL Compare engine will be upgraded in their next major version release, and also end their support for SQL Server 2000. These tools are: SQL Data Generator, SQL Doc, SQL Dependency Tracker, and the SDK.
SQL Backup, SQL Monitor, and SQL Multiscript will not be affected.