When Sam and Mikaela are running through the pillars to meet up with Optimus Prime there is a Decepticon that almost gets his head blown off. If you slow it down frame by frame on his right arm is says T1000. A little play on the Terminator. (DVD commentary.)
Shia LaBeouf's hand was seriously injured during a car accident. LaBeouf returned to filming, and the injury was written into the film as Sam damaging his hand falling out of the space bridge.
When the planes bombard the desert ruins, the explosion, which holds the Guinness record, took 8 months to be made, more than principal filming took! Also, the planes used while filming in fact bombarded the set, as explosives detonated for the massive explosion. Seems Michael Bay enjoyed the high budget of this film.
When Optimus Prime is being rebuilt/upgraded using parts from Jetfire, you can see a brief glimpse of R2D2 coming off of Jetfire (only visible for about 1 second, thus slow-mode should be used to see it, and it is permitted to use slow motion for trivia).
Before the release of the movie, an actual website called therealeffingdeal.com was set up with various posts by Leo. His final post, posted on the eve of the film's release, is that he is heading off to college and that he hopes his roommate "Isn't a total loser."
In one shot from the Predator's camera, we see a shot recycled from the first Transformers film of the desert attack.
During the library scene when they are running away from the girl, if you look closely most of the shots with Sam you can see a light colored hand bandage around his left hand from his car accident during filming.
This film holds the Guinness World Record for the largest explosion with actors involved put on screen.
When Sam starts drawing the symbols in his room, the first poster he draws on is for Bad Boys 2, another Michael Bay film.
When Davastator starts to suck everything up, there is a shot of a newspaper with a headline that reads, "Mysterious Robot Spotted". That robot is an old version of Shockwave.
This film started shooting one day after the first film won the MTV Movie Award for Best Movie.
The dog that Mikaela has in the garage that she calls Bones, is actually Michael Bay's dog, and Bones is his real name.