1. PCI slots. Peripheral Component Interconnect. Usually color coded as white. 2. AGP slot. Advanced Graphics Port. As the name implies, this is used for graphic cards that run off the AGP bus. 3. ATX motherboard power connector (Power Supply). 4. ZIF Socket. Zero Insertion Force. Where the processor goes. There are many types of sockets. Some motherboards have two sockets, which is called a Dual Processor motherboard. 5. Memory banks. Length/# of pins vary on the type of RAM the motherboard can use. 6. Chipset. (VIA, Intel, SiS, etc..) 7. Onboard controllers. Blue is IDE and the black one is Floppy. The color may change depending on the manufacturer, but they are all in the same general location and have the name right by it.
When Windows is installed it probes your computer for all installed hardware and installs the proper drivers. There are many drivers installed for a motherboard that are specific to the type of chipset, processor, RAM, and speed. When you install a new motherboard the settings and drivers for the old motherboard won't work with the new one.
Generally when you install a new motherboard you will need to reinstall Windows (you might get away with Repairing the installation but probably not.)