On a new system the case is usually chosen to match the motherboard, but on an upgrade the motherboard may be chosen to fit the existing case. Size is also an issue in some situations. While the form factor standard should be sufficient guarantee that a motherboard of the same form factor will fit in the case, it sometimes isn't. If you are planning to use a very large motherboard be sure it will fit in the case you are considering. Cases are available in either desktop or tower styles.
Tower cases are usually available in a wider variety of sizes.
This is largely a matter of personal choice, and matching to your furniture and space requirements. Larger cases provide more room for the components of the system, allowing for more expandability of the system. They also often produce a system that runs cooler, since components can be spread out. Many people find them easier to work in as well, since the components tend to be less cramped. On the converse, they also take up more room and cost more than smaller cases.