From Allearsnet:
"There have been many instances of people saying that Disney now pays no attention to these faxes. That is not true. As I said previously, all Disney resorts are different. Some room assigners are better than others just as some resorts are better than others. People like to rationalize the reason for their not getting their requests and it seems that this is an easy one to use. "
I do both- have it noted on my reservation and fax a request. It only takes a minute to do and it doesn't hurt to fax, so why not? The worse thing they could do is ignore it and you'd be no worse off.
Recently a CM from CBR posted on this site that they pay MORE attention to faxed requests than the ones noted on the reservations.