Ah, yes, this is what I thought you meant the first time around but wasn't sure -- yes, a close-to-full disk can produce some ugly disk fragmentation, even if the files are defragmented.
Having a disk that is close to full, though, is a bad idea I think that some people don't get. Hard disks are not static storage media anymore -- they're dynamic in the sense that they are ever-changing with general system use, and not just when you copy a new file onto it. It's a good idea to keep a good 20% to 25% of your drive free so that there is enough space to let the system move stuff around without being cramped for space. Back in the day, this meant leaving ten or twenty megabytes free, whereas today, with such large, cheap disks, this can mean leaving anywhere from 1 to 20GB free, and with hard drives already being advertised the way they are with more free space than you'll actually get, people don't want to believe that there's even MORE space on their disks they're not supposed to use.