I'm just going to bulk copy-paste from the d20pfsrd.com "Animal Companions" page, the part starting "Intelligent animals" (referenced to be from Ultimate Campaign):
"Intelligent Animals
Increasing an animal's Intelligence to 3 or higher means it is smart enough to understand a language. However, unless an awaken spell is used, the animal doesn't automatically and instantly learn a language, any more than a human child does. The animal must be taught a language, usually over the course of months, giving it the understanding of the meaning of words and sentences beyond its trained responses to commands like "attack" and "heel."
Even if the animal is taught to understand a language, it probably lacks the anatomy to actually speak (unless awaken is used). For example, dogs, elephants, and even gorillas lack the proper physiology to speak humanoid languages, though they can use their limited "vocabulary" of sounds to articulate concepts, especially if working with a person who learns what the sounds mean.
An intelligent animal is smart enough to use tools, but might lack the ability to manipulate them. a crow could be able to use simple lockpicks, but a dog can't. Even if the animal is physically capable of using a tool, it might still prefer its own natural body to manufactured items, especially when it comes to weapons. An intelligent gorilla could hold or wield a sword, but its inclination is to make slam attacks. No amount of training (including weapon proficiency feats) is going to make it fully comfortable attacking in any other way.
Even if an animal's Intelligence increases to 3 or higher, you must still use the Handle Animal skill to direct the animal, as it is a smart animal rather than a low-intelligence person (using awaken is an exception—an awakened animal takes orders like a person). The GM should take the animal's Intelligence into account when determining its response to commands or its behavior when it doesn't have specific instructions. For example, an intelligent wolf companion can pick the weakest-looking target if directed to do so, and that same wolf trapped in a burning building might push open a door or window without being told."
This text is usually my source in discussions of what an Int 3+ Animal Companion can and cannot do.
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Keep in mind that in order to learn a language, you have to be taught it (either through lessons or some serious immersion), thus the need for a rank in linguistics. Humans (hopefully) have higher than a 3 int, but that doesn't mean we know tiger, bear, dolphin, etc., because we haven't been *taught* it. Once an animal companion has been taught a language, that still doesn't mean it will automatically do what is being asked. Handle animal in this case is the druid/ranger/etc. getting the animal to do as asked. In a companion that doesn't understand the language, that means emphasizing the command in such a way that they'll follow it (think of dogs and how even when they know a trick, they will still only perform them for certain people, and not just anyone who knows the command phrase). In a companion that understands the language, that means coerce them into doing it (think a toddler that knows what you're asking, but doesn't want to do it. Not their parents = good luck!). So handle animal is still relevant, regardless of whether or not the animal understands the language, it just changes the flavor of how you're using it.