Because that's how hard drives work. You move and copy - often very large files nowadays - and fragments of data are left behind, muddying up the system. The question is how the system deals with it.
I actually believe that Windows 7 represents a real improvement on how memory and fragmentation are managed. Vista wasn't bad, either. They both do pretty well.
I think it's more that the registry and filesystem get bloated and crufty. You can defrag an older installation and it'll still be slow.
It happens on new systems too. I've done it dozens of times, install Windows and be happy about the fresh, fast installation. Install some apps so you can use the machine and it slows down. Office was always the worst, even on a brand new install.
I actually believe that Windows 7 represents a real improvement on how memory and fragmentation are managed. Vista wasn't bad, either. They both do pretty well.