A book discussing copyrighted and trademarked works can unquestionably be done. It has been done, many times; search on Amazon for unauthorized guide to and you'll see books on everything from Buffy to Barbie dolls. The only question here is, how much trouble is it to get permission? Do you even need permission to do a book which is, essentially, criticism and analysis?
I suggest consulting a lawyer, because even though this answer may very well be correct: Writing about something may well be legal. However, there's no way of getting around the fact that publishing a book like this would be using trademarked properties to make money. Even if it's not illegal, companies have to enforce their trademarks or they risk losing them. (Copyrights and trademarks are very different animals.)
At the very least, publishers might want to get permission, even if no money is involved, to avoid receiving a cease-and-desist. Knowing the answers to these issues would help smooth the way with potential publishers, although their legal department would likely deal with this once the book is sold. If you're self-publishing, however, wouldn't have that advantage.
Finally, since its obvious that this has been done and can be done (see that Amazon link), you could also attempt to contact the authors of other, similar reference works: See what they did, and how they did it. If nothing else, it will give you more information on the process.
