I'm on a verge of making house-rule about animal intelligence, but in some doubt of how I should do that...
Animals have intelligence of 1 or 2. "Anything with Int higher than 2 can't be an animal". They often have high wisdom and skill bonuses to represent their natural cunning, but still low Int stat leaves them with 1 skill point per HD. When roleplaying an animal I often bump into lack of crucial skills: some don't have Move Silently, some - Survival, some - Hide...
The world of nature is a harsh place, survival of the fittest. You are either smart, strong or eaten. So, real wild animals are all but stupid. They learn, risk, notice, communicate, experiment, remember, teach their young... Of course, they don't have deep language, don't write books, don't crack equations in mind, but still... They are not so int-impaired as d20 suggests.
Done with explanation, let's get to buisness.
1. Animals and animal-like creatures get Int scores equal to their Wisdom.
2. CR of such creatures increases by +1 (for CR of 1 or more) or twice (for CR less than 1).
3. That way animals and animal-like receive 2-4 skill points per HD instead of 1, but have Int of 11-14. Which seems unfair compared to many animal-like monsters with 6 Int. Because they should adapt even better.
1. Animals and animal-like creatures have new Int score equal to (6 x old Int score). That is 6 (for creatures with old 1 Int) or 12 (for creatures with old 2 Int). Variant: assign Int scores manually (from 1 to 7, see guidelines below), because different animals have wide range of intelligence and ability to learn, with predators and omnivores being the smartest.
2. Animals and Magical Beasts get skill points at rate of (4 + Int mofier) instead of (2 + Int mofier). Animal-like aberrations, oozes and elementals will have to do with their usual (2 + Int mofier) skill points (or that would change game balance too much).
3. CR of Animals, animal-like creatures and Magical Beasts increases by +1 (for CR of 1 or more) or twice (for CR less than 1).
4. That way animals get 2-5 skill points per HD, but Int score of lower animals seems more natural.
N. Creatures with changed Int score (from solutions I and II) get special trait based on their past Int score:
Primal Intelligence (Ex): for purpose of requirement for communication and special effects (such as spell effects, class abilities...) treat <this creature> as creature with Int score of 1(2). The creature still get skill points and feats as normal and uses its real Int bonus for various checks as normal.
That renders some hardcore shapechangers vulnerable to effects of animal-affecting abilities and effects... Could be a problem, but again - could be interesting. And there is some issue with wizard's familliar...
Solution III (by marphod):
1. Animals and animal-like creatures get skill points based on Wis modifier, not Int. That is (2 + Wis modifier) per HD.
2. Such creatures can have ranks only in following skills: Listen, Spot, Hide, Move Silently, Survival, Jump, Climb, Swim, Balance, Escape Artist. Other skills are off-limits.
3. Special feats can allow other skills or change effect of some skills (like this: Street Animal - survival checks apply to urban enviorment, not wild; Circus Animal - Tumble and Perform skills are allowed).
4. This solution gives animals and animal-like creatures 2-4 skill point per HD (CR should go up, as with other solutions). But there is some problems with augmented animals (familiars, for example). They will experience a drop of skill points for every HD after transformation (but will have a wider range of skills).
Solution II variant guidelines (based on non-animal monsters from MM1):
Int nonability : oozes, golems, vermin, assassin vine. Totally lack learning or creativity. Stimulus-reaction behavior. Animal analogue: jellyfish.
Int 1: ankheg. Just a little more then usual vermin. Dull due to its primitive nature. Animal analogue: spiders?
Int 2-3: spider eater, bulette. "Bulette attacks anything it regards edible. When it senses something edible (that is, senses movement), it breaks to the surface and begins its attack". Creatures of great strength for whom surviving is easy (or, again, too primitive to experiment). Animal analogue: brontosaurus, frogs, snakes, domesticated animals.
Int 4-5: otyugh. "Primarily scavenger that can eat any kind of refuse. Intelligent subterrain being sometimes coexist with otyughs: they dump their refuse in the lair of the otyugh, which generally refrains from attacking them". Not quite inventive, but can learn to use an advantage. Animal analogue: sharks, crocodiles, herbivores.
Int 6: hellhound, howler, kreshnar, remorhaz, griffon. "Although wild remorhazes prey on frost giants (as well as polar bears, elk, and deer), the giants occasionally train these beasts to guard their lairs". Cunning and crafty, thanks to smart prey they hunt. Often pack hunters. Good learners and can be trained. Tend to understand basics of language they live among. Animal analogue: canines, leopards.
Int 7: behir, manticore. These creatures often have language, non-survival knowledge and hobbies (for example, collecting shiny objects). Can learn to use devices and tools. Animal analogue: ravens, parrots, killer whales.
CR changes: with this variant animal's skills go up only with Int of 6+, so CR for animals (and magical beasts) with 5 or less Int should stay the same. Note that individual animal can have different Int than typical.
So, is it OK or not?
EDIT: third solution added.
EDIT: added variant to second solution (thanks, jeweldevil)
EDIT: added guidelines for manually assigning Int score to animals.