I have a few different instances (SQL 2000, 2005) with indexes placed in a separate filegroup. Do i need to ensure that this group is backed up, or will it be rebuilt by a restore of of the database?
The first point to consider that a clustered index is actual table data. So in that alone, I'd say yes. Your whole database should be backed up and able to restore (there are a few exceptions to that, like read only filegroups that are subject to no DML).
The second point is that restoring a database does not rebuild or reorganize any indexes.
So yes, you should be backing up all of your data, indexes included.