Here's my two cents worth on this...
Pdfs:
You can make an argument either way regarding the inclusion of pdfs into the categories with print material. From one standpoint, print products are more popular because of higher visiblity and therefore are more likely to win. For example, let's say the five nominees for best supplement are: Book of the Righteous, Path of the Sword, 101 Spellbooks, Mercenaries, and Great Aspeigh. Of those choices, it is very likely that the two pdfs will likely not win because of the familiarity and visibility of the other books. On the other hand, one can argue that inclusion of a pdf into a field of some many good nominations really speaks volumes about the quality of the pdf itself. As much as I would like to say create a separate category for pdfs, I believe most publishers want their pdfs to compete against the print products because it will give them a boost should they be nominated.
Giving Awards:
Since only 5 products are nominated per category, there should only be a single winner and no second or third place announced. However, if the number was increased to seven or eight products, then a runner-up certificate (not a trophy) could be issued.
Special Awards:
OGL Only: I like this idea immensely. There are a limited number of possible nominees this year, but next year's awards look to be more in terms of possible numbers if everyone comes through with their releases.
Judges Choice per category -- bad idea. This is what the nominations themselves are.
Judges Choice overall -- choosing a single product that all judges are in agreement represents the best the industry offers in terms of overall quality, layout, editing, writing, artwork, mechanics, and useability. The best of the best. This would probably be the best idea to work with.
Publisher's Choice -- This could be an interesting award if approached properly. Create two categories (PDF of the Year, Non-pdf of the Year -- or something like that) and allow only publishers to submit votes. However, you should not limit exactly who can vote in terms of numbers of publishers. Only one representative from a company could vote but all publishers should be given the opportunity. You could set the prerequisite of publishing at least 3 products during 2002 in order to be eligible to vote. This would disqualify brand new publishers and those who have only ever made a single pdf from voting. If you've done 3 or more in 2002, you're showing a commitment to publishing.
Voting in general:
Despite the skewed results of last year's outcome, I do not believe you will see that so much this year. There have simply been so many GOOD products released (Nyambe, Oathbound, Book of the Righteous, Mercenaries, FFG's path series, Spycraft) against the fact that Wotc's output has been reduced considerably compared to 2001. I think the field is starting to level itself out without excluding Wotc. This year's vote will give us a more accurate picture. If Wotc sweeps again, then perhaps adjustments should be made.
Just my opinion.