Microsoft Knowledge Base Article 824125 contains the following summary:

This article describes how to replace a motherboard on a computer that is running Windows 2000 or Windows Server 2003. Two typical reasons for replacing a motherboard are to upgrade an existing one and to replace a failed one. In either case, you must reconfigure Windows to work with the new motherboard and its components because not all motherboards use the same hardware abstraction layer (HAL), integrated device electronics (IDE) controllers, basic input/output system (BIOS), and other components.

The following are two scenarios that describe the steps that you must perform to reconfigure Windows to work with the new motherboard. Follow the steps for the scenario that is appropriate to your situation.