IMHO, it depends. If you don't have some version control to rely on, it can provide extra documentation to someone. Let's take a trip to the real world: you have a long script which processes files in different loops in different ways, and some PHB says, don't 'blurk' the 'B' files, and you figure out that that means changing this:

for $filename (@filelist) {
  ...
[download]

to this:

for $filename (@filelist) {
 # PHB doesn't want B files blurked
 next if $filename =~ /^b/i;
...
[download]

A week later some other PHB is asking why the B-files aren't being blurked, and grudgingly gets the other PHB to agree that it should be changed back. Do you comment out that line, or delete it?

Two weeks later they decide that they really do want the b-files blurked, and you're out on holiday or have quit to preserve you sanity, and some other programmer who is not too familiar with the code has to figure out what exactly needs to be changed. It may be a poor man's CVS (which is odd considering CVS is free), but that commented out line really helps him, and he buys you a beer when you get back. The trick, of course, lies in knowing what should be commented out and what should be deleted :-)