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Trevor_Blake comments on Recommended reading on the ethics of Animal Cognitive Enhancement - Less Wrong
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Humans have bred wolves into dogs and dogs into specific breeds of dogs. Many of those breeds of dogs have a more human-like intelligence at minimum and are perhaps also more intelligent than they might have been without humans having bred them. Everything about the ethics of dogs as pets, servants, weapons, experimental subjects, commodities and strays is a non-hypothetical case study of animal cognitive enhancement.
The comic book WE3 by Grant Morrison (soon to be a film?) addresses animal cognitive enhancement. Recommended. The villain Gorilla Grodd and the hero Gorilla-Man are uplifted great apes in comic books.
The Planet of the Apes franchise applies as well. The most recent film is exceptionally recommended.
The Island of Dr. Moreau, of course.
The Cat in the television series Red Dwarf.
If you include humans as animals, there's all that literature too.
I have not seen any evidence of dogs being more intelligent than wolves.
In fact, I remember reading that wolves are more intelligent than dogs, but I can't find the source right now.
AFAIK, wolves engage in more independent thinking - they solve problems on their own - and dogs engage in more dependent/tool-using thinking - they try to get humans to solve problems for them.
It's also been said that ancient humans were more intelligent than modern ones. In fact, both the argument for human intelligence and the wolf-dog argument have put forward the idea that being domesticated lowers intelligence (in the case of humans, it can be said we domesticated ourselves). I don't really think this is a simple hypothesis to investigate at all given the complexity of investigating intelligence.
Some references:
News Article on Human Intelligence--News article discussing this hypothesis.
Gerald Crabtree--This is the researcher I've seen quoted a lot lately on the idea that ancient humans were more intelligent than modern ones. From the article above, and looking at his published work, it sounds like this is just a hypothesis he wants to test, rather than something that he has thoroughly investigated.
News Article on Dog-Wolf intelligence--This news article has some discussion of an experiment trying to determine differences between wolf-dog intelligence.
A human can teach a dog to perform a trick much more easily than it can do that to a wolf, which is the standard test of (human-useful) intelligence for canines, and variations in trick-learning ability are massive between breeds.
Perhaps a wolf is simply less cooperative with humans.