OK, it sounds like you are specifically having a problem with a player that seems to be trying to annoy you with the skill. Heh - First piece of advice is put the die down and take a deep breath. (No, I don't really think you are that peeved.)
But seriously, he is trying to spend points in the skills and then make use of them. Even with four monster books, I would argue that it is possible a PC might have a Savant type knowledge of everything out there. Heck, how many gamers have stuff from the MM near memorized? Or any other rules mechanics? My point is that the PC is sinking the points in the skills, so they should be useful. However, there may be times when the DC is higher than normal.
Commentary below
Mystery Man said:
Let me give you an example of how he goes about this. First he wants to know if its a abberation, magical beast or whatever so that he can roll the correct knowledge check. I think that that should be his first roll. Roll a knowledge check and if its the right one then you can roll to see if you know anything about it. Make sense?
*nod* OK, try a different tactic. You have the PC's skills right? Make yourself a little cheat sheet of what skill bonuses he has, with the type of creatures that it applies to. When the PC's encounter something odd, and the Player asks what kind of creature it is, just have him roll a D20. Then, you can look at your cheat sheet, modify it by the appropriate skill (if any) and tell the Player what information the PC knows.
The Player may object since he doesn't know what skill you applied. Rationale is that the PC doesn't know what skill to apply, he just knows if he recognizes it. This will cut the metagame level of the Player figuring out how many HD the creature has and what kind of creature it is, based on the question and the roll.
Commentary on setting DC's - OK, I do not always assign the DC as stated in the book. Nor do you have to. Remember, the DC's for the Knowledge skills should be dependent on your gameworld, not what is in all the possible monster books.
If you decide that Bullettes and Owlbears are a recent invention of a mad wizard, then there is no amount of knowledge skill that will apply. Even if the monsters were in the books, they are a recent addition to the game world.
If you decide that a certain creature only exists at a specific oasis in a remote desert, then the DC for having any information for the creature will be higher than normal.
This is not nerfing the PC skill. It is helping to make your world a little more consistent. Just don't use these tactics every time.