Don't put your documents in the Preferences folder, for instance. If one folder node goes bad, all the folders within it could be affected. When the computer is trying to write a file, if it can't write it continuously, it has to lift the head and continue writing in a different location. That may happen quickly, and it keeps track of where the various pieces are. But as the number fragments increases, the drive gets slower.
Fragmentation happens on every machine.
Depending on the size of the file, it could be in the range of 1 to 1,000. If you're a novice, repairing fragmentation is something you should have someone more experienced do, and you should always have your data backed up before doing it. Using Norton Utilities 3.0's Speed Disk to optimize has resulted in truncated files. This problem has been fixed in version 3.1. You should always make a backup before doing any type of major restructuring of the hard drive.