When you are reading and running an adventure, do you like the stat block right there? Would you rather not have to deal with the stat blocks until you are ready for them?
Do you like the stat blocks right where the room and the encounter is described so you don’t have to flip pages? Would you rather it be in a different file, letting you split screen/print out the monsters?
Jon Brazer Enterprises 
I answered “throughout the adventure”, but the more accurate answer is “yes”.
In the encounter, I like a minimalistic stat block that gives me enough to work with. I often don’t need the full stat block (the feat and skill entries can be greatly abbreviated — I don’t care about the total bonus to Knowledge checks in a fight, and it’s enough to know that the Will save is +9, I don’t care that the creature has Iron Will), just enough for what is happening now.
In an adventure it’s nice to have the full definition at the back of the book. That way I don’t need to drag along every monster book (or worse, go out and buy… hang on, I like buying monster books) to support the adventure.
Having them all in a separate book makes it better for general reference, since I can then reduce the number of books to look in to find it when I’m not looking at the adventure, but want to find the ice lizard I remember from an encounter.