Faculty are writing lots of recommendation letters right now. One of my colleagues went to extra effort to print his letter, sign it, scan it, and then upload it. Unfortunately, this was counterproductive.
If you are requested to provide a letter in PDF, provide the original PDF that was created by your word processor or typesetting program. Don't scan the document, which makes it much harder to read. You don't want eyestrain (or anything else) to lessen the impact of your letter. You can either insert a PDF signature, or have just a typewritten signature; no one really cares whether your signature is on the letter.
Another irritation I have seen: don't use "watermark" letterhead that puts a large, dim image (for example, of the university crest or logo) behind the text. Some people apparently think this looks cool and sets their letter or institution apart (MIT CSAIL, I am looking at you), but in fact it makes the letter harder to read without impressing anyone.
More advice on writing a letter of recommendation appears at http://homes.cs.washington.edu/~mernst/advice/write-recommendation.html