Well, they are made by 2 different companies. Also, they have different features, settings, programs, compatibilty and options. They are the same in some ways, but different in others. Apple Computers (Mac's) are thought to be better than Windows Computers, but this is only certain people's opnions. Anotehr difference is that Mac's apparently also run better, but the noticeable difference, isn't about the Computers themselves, its more about the Price!
Another, more important thing is that Apple Computers are normally used for composing and making things, like music, programming etc etc.
Also, for the last few years apples have been able to use windows applications without the use of emulators. There is now a program called bootcamp that allows you to partition your hard drive to include leopard and xp or vista on the same computer.