This is what it says in one of the documents from the link that Steve put here.

MULTIPLE INSTANCES

SQL Server 2000 includes a multi-instancing feature which allows customers to install SQL Server more than once on a server. This is used in hosting and multi-application environments, for example. Customers using SQL Server Standard Edition must fully license each instance server (whether in per-seat or per-processor mode). Customers using SQL Server Enterprise Edition can install an unlimited number of instances on each machine without requiring any additional licensing.

So i think that yes, you would need to licence each instance.