How many bonus types are there?
Are there any rules to what casters can affect which bonuses?
It all comes down to stacking rules..
I have a creative player in my game that would like to create new spells and I would like to make a ruling on how each class can affect the game.
Bard
Resistance - resistance bonus
Heroism - morale bonus
Rage - morale bonus
Haste - Dodge Bonus plus an unamed bonus to attack
Clerics:
Resistance - resistance bonus
Guidance - competence bonus
Bless - morale bonus
Prayer - luck bonus
Aid - morale bonus
Magic Vestment - enhancement bonus
Magic Weapon - enhancement bonus
Holy Aura - deflection bonus
Divine Power - luck bonus
Druids:
Guidance - competence bonus
Resistance - resistance bonus
Shillelagh - enhancement bonus
Barkskin - enhancement bonus to the creature's existing natural armor bonus
Magic Fang - enhancement bonus
Wizard/Sorcerer
Resistance - resistance bonus
Mage Armor - armor bonus
Shield - shield bonus
True Strike - insight bonus
Magic Weapon - enhancement bonus
Haste - Dodge Bonus plus an unamed bonus to attack
Heroism - morale bonus
Transformation - competence bonus
Here in this thread.
But that just points you to this d20 SRD thread.
James Jacobs once said that it's unfortunate that this list got left out of the core rules, so I guess it's official, it's unfortunately not in the book. Might as well use the d20 SRD then. I'm mostly sure all those same bonuses are applicable in the same way in Pathfinder.
As for limiting which classes can use which bonuses, that might get awkward. For example, if you rule that a certain class cannot cast spells that create a certain bonus, you might end up going through all of the spells, one at a time, and changing bonus types on some of them to accomodate this ruling. Or even more painfully, moving a divine spell to become an arcane spell, or vice-versa, if necessary.
And don't forget that new spells are coming out all the time in the various APs, Companions, and other sourcebooks.
Instead of limiting effects by class, why not limit effects by, uh, effect? By that I mean, if a spell's effect is to magically enhance some characteristic, then that should be an enhancement bonus regardless of which class casts that spell. If a spell helps you avoid fire damage, then it should be a resistance bonus, regardless of who cast it. And so on.
When a "creative" player decides to create a 1st level arcane spell that fills him with hope and elation to grant him +4 AC as a 'morale' bonus, and then promply stacks it with Mage Armor and Shield for a net +12 to his AC, we might have broken the system. That sounds a little bit over the top. Especially when he researches another new spell that gives him a +4 'luck' bonus to his AC, and another new spell that gives him a +4 'insight' bonus to his AC. It's even possible that you as a DM ruled that wizards should be able to cast spells with morale, luck, and insight bonus types, so he would be entirely within your ruling to use these bonuses. But +20 to his AC at level 1 is ridiculous (and more ridiculous when he takes Craft Wand and makes wands of these spells to free up his slots).
You have to draw the line somewhere.
Drawing the line as a class restriction won't work. A "creative" player will just work within your class restrictions, as in my example.
So you should draw the line as an effect resriction. Spells that increase your AC are either 'armor' bonuses that don't stack with other 'armor' bonuses, or they are 'deflection' bonuses that don't stack with other 'deflection' bonuses. If you do allow other bonus types to be applicable, then they should give smaller bonuses or require higher level spells, or both.