Well, this is bound to make me the most unpopular person here, but this is what I think based upon my experiences at all ends of the spectrum.
Following up on a comment that Morrus said about the awards being closely tied to Gen Con now, one thing that should be kept in mind for future awards (since it is too late to implement it this year) is establishing a roadmap or timeline for future and additional award categories or classifications to ensure growth. This will allow for adequate time to clearly define the qualifications that allow a product to be nominated in that category. For example, if you know that next year you will be adding Best Miniature Skirmish Rules, you will be able to iron out exactly what is a miniature skirmish and what games qualify. Would this category include D&D miniatures, Warmachine, HeroClix, Mage Knight, and Mechwarrior? What about Warhammer or Void? Rather than waiting just weeks before nominations are to begin, by having a clearly defined timeline, you give yourselves ample time to iron out the bugs and look more professional.
Secondly, the awards need to be structured so they will recognize quality of all eligible products and not from just those submitted by participating publishers if the awards are going to become more of a true Gen Con event. As it stands, d20 Guide to Widgets could be the hottest, best-selling and most critically acclaimed book on the market but if the publisher does not choose to send 5 copies to the judges, then it cannot be considered for nomination. If the Ennies are going to evolve into a majorly recognized award among gamers rather than the 'fan club' award it is now (and that is NOT meant to be derogatory), then it needs to find a way to become more inclusive.
At this point in time, the only way I see for that to happen is to remove the judges altogether. Online gamers have already demonstrated time and time again that they are very product saavy and know what is going on in the gaming world. They have a good picture as to good products and bad products and don't necessarily need to be told by a judging panel which are better. Nominations could be done via a write-in vote like those done at Pen & Paper. The top five vote getters for each category would then move on to the final voting rounds where new votes would be cast by the voting public as normal, thereby determining a winner. By structuring the voting in this manner, you will likely see a reduction in the number of nominating votes a product receives, but you will see a much greater diversity of selections that could very well include some surprises that otherwise, would have never been considered.
Now my thoughts regarding the categories.
Best Adventure - This should be open to both print and electronic submissions (including free products).
Best Campaign Setting - I would urge inclusion of both OGL and non-OGL settings for this category. It shouldn't matter in this circumstance whether the setting is open.
Best Setting Supplement - In order to qualify, the nominees should have the name of the setting either included with the title or printed as a graphic logo on the cover. For example, Silver Marches (Forgotten Realms) or Oathbound: Wrack & Ruin.
Best Interior Art
Best Cartography
Best Cover Art
Best Graphic Design and Layout - These four should be separate but recognize the product AND the individuals responsible.
Best d20 Game - Needs a clearer definition of what separates this category from the others. When you look at the many d20 releases, most fall into either campaign settings or rules supplements. When I think of a d20 game, Spycraft, Mutants & Masterminds, and Babylon 5 come to mind because there are radical fundamental changes to the d20 system that form innovative mechanics associated with that setting.
Best Rules Supplement - Should exclude products that qualify for Campaign Supplement but be open to both OGL and non-OGL entries.
Best Monster Supplement - This one should be open to both OGL and non-OGL entries.
Best Aid or Accessory - This seems to be a catch-all category to cover anything that doesn't fall into the others. Here we would have such things as DM Screens, Miniature Carrying Cases, Battlemaps, etc. Is this a category that is needed at this time or would it be best served by adding it at a later date once it is more clearly defined (see my first point above).
Best Non-Open Gaming Product - This should be dropped. Open the other categories up to allow them to compete on a level field.
Best Electronic Product - This also needs to be dropped until it can be better defined in terms of what qualifies or split into more specific categories (see below). For example, does eTools qualify since it has been successfully patched by CMP, making it a different program? What about PCGen and the changes made to incorporate 3.5?
Best Free Product - Again, dropped.
Best Resource Fan Site
Best Official Site
Best Campaign Fan Site - Combine all three into a single Best Website.
Best Publisher - Fine as it is.
Ennies Peer Award - As much as I am in favor of a Peer Award, it really has no place in an awards that is driven by fan votes. The Origins is looking to develop into a peer award system. Let's leave it to them for the time being. The biggest problem behind the peer award as it worked last year was only a select number of people who work within the industry were even aware of it. If you are going to make a Peer award then it has to be something ALL industry professionals have a say in.
Additional categories discussed:
Best Writer - It isn't necessary to determine who wrote what part of a book in order to have this category. You nominate the book for the writing AND the writer or lead developer (if more than four people are involved). All you have to do is look at the credits page (the same goes for art and cartography).
PDF awards (if a product is released as a print product during the same qualifying year as the pdf, it is not eligible for a pdf award).
Best Electronic Rules Supplement - This would cover things like monster books, new PrCs, exapansions of existing core classes, etc.
Best Electronic Campaign Setting or Supplement - Combines the rules for the two print categories into a single category for pdf.
Best Overal PDF Product - PDF of the year.
As a final note, I think any revision work should be allowed to be considered if it is presented as a new product (complete with new SKU). As Chris Pramas pointed out, an incredible amount of work goes into conversion from 3.0 to 3.5 and I have yet to see a product that doesn't illustrate this. Book of Fiends should be considered as should Complete Book of Eldritch Magic because they reflect a great deal of work on the part of the design team to make it a better book and not just a straight conversion. To state that any conversion book is ineligible is unfair to all of those folks who put their own blood and sweat into making it 3.5 compliant.