I have to agree that many of the GRE chem questions were harder than they needed to be, but they are trying to separate a group of already exceptional students.
The biggest fault of the Chem GRE test is that only one composite score is reported; the score isn't broken down based on subject (e.g. organic, inorganic, physical). Say a student kicks ass at organic, but hasn't taken a physical chem class yet. They wouldn't do well on the exam. I'm certain that professors take this into account when they review applications. I think it's better to think of the Chem GRE as a test to ensure that you really do have the knowledge of chemistry that your other application information suggests. It's more of a verification than anything else and I don't think that it plays a huge role in your application process (provided you have a reasonable score).