Many journalists have got the name wrong, and apparently some characters refer to the dark side of the moon, but I can't find any evidence that Transformers 3 was ever named Dark Side of the Moon.
The earliest Google News result for "Transformers 3" and "dark side of the moon" is OnTheRedCarpet.com from September 12, 2010 and says:
"Transformers 3", aka "Transformers: Dark of the Moon", the latest film in the hit ... the dark side of the moon, confirming that mankind is not alone in the universe.
The end of the trailer shows the current title as well.
The next results are all from 6th, 7th and 8th October 2010, after the title was first revealed. CinemaBlend.com from Oct 6, 2010:
Transformers 3 To Be Called Transformers: The Dark Of The Moon
If you thought titles didn't get much worse than Transformers: Revenge of the Fallen, brace yourself, because it looks like the third movie is going to be called something even more ludicrous. Collider confirmed today that the movie previously known only as Transformers 3, will bear the title Transformers: The Dark of the Moon. No, not The Dark Side of the Moon-- that would make too much sense. It's just The Dark of the Moon, and other than being a vague nod to the extraterrestrial origins of the Autobots and Decepticons, I have no idea what it could possibly mean.
Collider said earlier the same day:
The Title of TRANSFORMERS 3 Is “TRANSFORMERS: THE DARK OF THE MOON”
Transformers 3 now has its official title and that title is: Transformers: The Dark of the Moon. TFW2005 first discovered the title through the listing of some upcoming movie tie-in novels, “Transformers: The Dark of the Moon – Secret of the Autobots“, “Transformers: The Dark of the Moon – Autobots Betrayed!“, and “Transformers: The Dark of the Moon: Invasion of the Decepticons” (all three novels are set to be released on May 17, 2011). We have now confirmed the title with sources close to the production.
Even earlier that day TFW2005 said:
Transformers 3 Title Revealed?
Some upcoming books listed at the Amazon revealed what might possibly be, the Title of the 3rd Transformers Movie.
The books are to be released (May 17, 2011) very near the release date of Transformer 3 (July 1, 2011). The author of the books is official and has written books for the 2007 Movie and ROTF. The publisher is none other than HarperColins, which produced similar books for both movies.
No need of spoiler tags, here's the possible Transformers 3 Title...
Transformers: The Dark Of The Moon
Update (Yes, an update already) : There is a movie website domain name registered on 13th September this year. It's www.transformersthedarkofthemoonmovie.com. The domain is registered by the same people who registered both the 2007 Transformers movie and ROTF Domains on behalf of Paramount & Dreamworks.
TFW2005, Bringing Transformers 3 News... First!
Hmm, well seems OnTheRedCarpet.com knew the name in advance, a day before the domain was registered in September, but strange the other sites didn't cotton on when it was big news in October. Surely they will have seen the same teaser trailer (though perhaps the actual trailer video was updated later). And it's possible they went back and put in the full title once it was known, as others have done.
In any case, I don't see any evidence for Dark Side of the Moon.