Yes, there have been messages hidden in Disney movies. No, I do not believe they were subliminal; they were nothing more than harmless fun or an artist's personal statement. The implication that The Walt Disney Company is conspiring to manipulate the public is, in my opinion, baseless.
This conclusion is based on my Webster's New World College Dictionary's (Fourth Edition, 2000) definition of "subliminal" as "below the threshold of consciousness or apprehension; specifically, involving the use of stimuli intended to take effect subconsciously by repetition."
I know of several instances of messages in Disney films that could be considered "below the threshold of consciousness or apprehension," but none meet the second part of the test: "intended to take effect subconsciously by repetition." If they are subconscious, there is no evidence they would even have an effect on the viewers.
Why include a message at all? I can think of three basic reasons:
A tribute to an admired person or favorite artist. The animated TV series "Kim Possible" contains an episode with caricatures of the show's producers. The Pixar animated feature "The Incredibles" has a scene with caricatures of two of Disney's most beloved and talented animators: Fran Thomas and Ollie Johnston. The 1938 animated short "Ferdinand the Bull" is full of caricatures, including Walt Disney as the matador. These examples (which I have seen myself) are all obvious and are in no way subliminal.
An inside joke among artists. These are usually subliminal. One example would be the reported case (which I personally have not found) in the animated feature "Who Framed Roger Rabbit" in which Jessica Rabbit's dress quickly flies up and she is wearing nothing underneath. Another example (which I did see) was a brief moment during the wedding scene in the animated feature "The Little Mermaid" in which the minister becomes aroused. And in "The Lion King" supposedly the letters SEX can be seen. These all seem to be jokes. In the case of "The Lion King," I have read that these letters are actually SFX, the calling card of special-effects artists.
An act of defiance by a disgruntled artist. The best example of this was the Topps 1977-78 series of Star Wars trading cards. An angry artist drew an obvious anatomically correct C-3PO, submitted it (along with his resignation) and left. We know about this because the artwork was so obvious that no one noticed it and the card was issued, much to Topp's embarrassment. If such an artist wants to embarrass a company, the message by definition would not be subliminal.
Why would The Walt Disney Company allow subliminal messages in their movies? There is no practical reason why they would. It is very difficult to manipulate the public, and the risks of being discovered are too great. I am a Disney fan and collector myself, and I have been to collectors' conventions where animators have described how thoroughly their work was being examined. For example, in the animated feature "Pocahontas" one artist told how he was forced to remove Aladdin's lamp from the background in the raccoon Meeko's burrow.
Why has so much publicity been devoted to possible subliminal messages? I can think of only one reason: the furtherance of political and/or social causes by advocacy groups. If one of these groups can convince its followers that a major corporation is manipulating the public, donations are sure to flow in. (I would put the recently imagined "War on Christmas" in this category.)
So if you hear of a message in a movie especially a Disney movie look for the joke (or tribute) and not the conspiracy.