I don't have a problem with awards, but there should really be some guidelines to make sure everyone of roughly equivalent talent has an equal chance of winning. If I were making fanfic awards, I'd do something a bit like this:
1. To help weed out fics that have gained a heck of a lot of attention already, I'd put a "cap" on the date when the fic was finished/last updated - for example, while the fic could have been started anytime (to be fair to people like me who write slower than a turtle on Valium), it would have to have been finished or last updated in, say, the year 2006 (and not counting rewrites and revisions of things written prior to 2006), effectively pulling the plug on the endless nominations of stuff like Acey's Pokemon MASTER, which was finished years ago and is STILL talked about in gushing tones.
2. One shots, in progress fics, and finished chaptered stories should have separate categories. Among these separate categories, much like there is for dog shows, there would be certain "classes" - for example, a category in each main heading (One-Shot, In Progress, Finished Chapter Stories) just for things like Original Trainers, Pokemon POVs, Romance/Shipping, Pokemorphs and Shapeshifters, Action, Fantasy, and perhaps for fics that don't fit these common genres but are set in certain canons, such as Mystery Dungeon or Pokemon Special. The winners of these "Best in genre" categories could then move on to be judged against each other in a "Best One-Shot of 2006," or whatever.
3. To keep it from being a popularity contest, the position of winners would be determined by judges that can be assumed to be impartial. For example, while I write and read a lot of Pokemorph fiction, and it's what I am mainly known for, I do not write, or usually read, Original Trainers. Because I am pretty much impartial towards OT fic, I would not be familiar with most of the authors, and would be able to judge less on the author's popularity and more on if I feel the writing, characters and plot are any
good. If finding impartial judges seems like an impossible task and people would rather stick to taking a vote, there could be "weighted votes" - say, a vote for an exceedingly popular author could be be worth only half of what a vote for an author who doesn't have a rabid fanbase nominating them left and right is. Though that second option could be seen as a bit unfair, as
some authors are popular because they really are good and really do deserve it.
4. If weighted votes seemed too unfair, or impartial judges seemed too impractical, perhaps an award could be made exclusively for authors who do not have a lot of publicity (with perhaps another award open to everybody). Fics which would be exceedingly well known to just about anyone who browses here or the Pit of Voles (Fanfiction.net) with any regularity would be strictly banned from nomination for this particular award, leaving it open only to us lesser known folk who would never hope to win anything otherwise ^_^'
