I read this page, and it is very well thought out. I have to applaud the author for the effort and logical functions they have put into their arguement. While a good chunk of it is questionable in my mind, the basics are very intriging. I like the idea that the Hufflepuff cup is in the trophy room, whether transfigured or not. The part that I find a little weak is the references to the secret passageways and suggested correlations between the mentioning of transfiguration and the trophy room as reasons for the location of the cup.
I don't believe that the secret passageways are a reason for it's location, but if correct, they could serve as a vital resource for Harry during the ultimate showdown. As for the mentioning of transfiguration at times related to the trophy room, this could really just be a coincidence. When we try to think of the locations within Hogwarts that are mentioned frequently enough to draw attention to them, while not being main areas of action (commonroom, Great Hall, Library, Forbidden Forest, the girls bathroom, the lake, etc.) we are left with the trophy room, various classrooms, the owlrey, and probably more ... are they of great significance or are they just locations where Harry et al. inevitably will visit during their years at Hogwarts?
With reference to Peeves and the trophy room, it is possible that it is just a convenient location to mention ... a lot easier to say "the trophy room" than "the hallway outside the kitchen" or "the stairwell under the North Tower" for instance. Peeves can only "bounce around" so many location and it is possible that he just prefers the trophy room without implying any importance.
Some may say that this argument is just as vague as some of the ones mentioned on the link, and I will agree whole heartedly. I'm not attempting to discredit her argument, just pointing out that it may not be as ironclad as some of the other plot predictions floating around.
I guess, at the end of this ramble, I am saying that I really like the trophy room/Hufflepuff cup scenario, just not for all of the reasons listed on that page. I think her most important connections are numbers 9 and 17 in her list. They really struck a chord with me and seemed to follow along with the way in which JKR has been writing throughout the series.