Let's see, if I go with just the stuff I have purchased since starting D&D3e, the list is surprisingly short. If I include stuff from before that, well, 25 years as a collector has meant quite a few stinkers.
For d20 books, I would have to agree with a number of people and say that the Creature Collection I was the biggest disappointment. The production value seems rushed and things were missing from it or were grossly inaccurate (hit dice type comes to mind). Plus, the art in the book, and I use that in the broadest sense imaginable, leaves a great deal to be desired. I do not think I have used a single thing from that book.
I have a minor level of disappointment with Relics and Rituals, but that is mostly from my not looking through it the way I normally would. I was hoping for more things to inspire my creation of cleric sub-classes and divine magic items. While I have used or modified some things from this, I would say it is the least referenced book I have used.
Another book I completely regret getting was, I am happy to say, only $5.00(US). That was the cover price! It is by a fairly major publisher (the name escapes me), and it is a sampler of several of the books they publish. All I know is that the material presented was so uninspiring that I came away feeling like I should ask for my time and money back. I am thinking of giving this one away to someone outside my gaming group. I don't want any of them to know I bought this swill!
Unlike others in this thread, I did find some good use out of Dieties & Demigods. The temple maps have seen use, and the drawings of the holy symbols have proved handy. The use of an avatar for the dieties was a nice mechanic, and I plan to use that soon. I would have liked more descriptive text on the D&D Pantheon, explaining the relationship of the dieties to each other and to the mythos of the pantheon. I would have also liked more information on different types of religions and creating your own, but I have GURPS Religion for that. So, I do not regret getting it. I do sort of wish I had paid less, but then I am cheap.
Otherwise, I think that is all. I do not own many 3e books, and I don't own any 3.5 (I don't think). I am been selective on my purchases, so I have missed a bunch of the real stinkers.