I really don't like jumping into threads like this because the definition of what is "best" and "worst" often depends on what the player (of DM) wants.
For example, many people hated Dieties and Demigods, because of the focus of diety stats, and lack of worship information. I however, generally liked the book because diety stats were exactly what I wanted. As I've mentioned before I enjoy epic games. After reading the Iliad last year in mythology class, I envisioned a setting where the gods were very petty and often intervened in mortal affairs (like the Greek Gods). In a lot of mythology characters challenge, even occassionally defeat the gods. Hence, the necessity of diety stats my campaign. Of course, DMs who prefer the gods to be distant entities who rarely intervene in mortal affairs will find little use out of the book. It all depends on the campaign.
Also, I hated Manual of the Planes because I dislike the "great wheel" cosmology, which always seemed too tied to the D&D alignment system for my case. I was looking for a toolkit for me to build an alternative cosmology, not a rehash of the "great wheel" concept. To DMs who loved the "great wheel", this was a great book, but to me it was not.
Same goes for splat books. Prestige classes that are "boring" for some, might not be for others. Some prestige classes might be overpowered for some campaigns, but for high powered and epic campaigns they might fit right in. Really, I think it's all just a matter of opinion and circumstance.
