Here are some subtle things seen during Dark of the Moon. Do not continue reading if you have not seen the movie. Slight and major spoilers after the jump. Also, I have decided to hold off on my full review for about a week because more people will have seen the movie by then. I have also updated the Character List page.
Sentinel Prime is red throughout the entire film, unlike the announcement trailer where he was yellow.
At the very start of the film during the Cybertron battle scenes: On the far right of the screen you see a huge 4 legged Transformer which is a giant Ravage model
Sam's car has the same mirror ball & Bee-Otch air fresher that Bumblebee had inside him in TF1
Jerry mentions Pink Floyd and "The Dark Side of the Moon".
When the man is pushing buttons on the copy machine (Laserbeak), it is the tune "More than Meets the Eye"
When the Decepticons land from the Spacebridge to the right of the screen you see one scan a garbage trash truck & turn into it. As it drives off you see 2 identical large red fire trucks implying they are also Decepticons
The Government sending the Autobots away from Earth on a shuttle is straight from a G1 cartoon episode called "Megatrons Master Plan"
A giant Spacebridge to bring Cybertron to earth is straight from a G1 cartoon episode called "The Ultimate Doom"
Primes axe that he uses against Megatron at the end is from the original G1 pilot cartoon "More than Meets the Eye"
The white private jet you see in several shots behind Sam & the government woman has 4500X on it,
This is the same number Blackout had on him in TF1 and it is also the number of Michael Bay's private jet (It may even be his jet)
When Bumblebee transforms for the last time at the end of the film he clearly makes the G1 cartoon transforming noise (Laserbeak also makes a slower version of the sound when he transforms from photocopier to bird)
When the humans are being shot by the Decepticons watch for a humans skull to fly off and bounce down the street
When the Autobots are taken as prisoners during the final battle, it's Barricade that is restraining Bumblebee. You see him for the next few minutes
Sentinel Prime's line "The needs of the many outweigh the needs of the few" is homage to the same line spoken by Spock in Star Trek 2. Spock and Sentinel are both played by Leonard Nimmoy
CISCO have a lot of product placement in the film, several times you will see Cisco units with HUGE Cisco logos on that they wouldn't usually have. Also EVERY computer & monitor in the film is lenovo again with name badges on they wouldn't have. (Dylan does have an iPad though)
Another Spock reference is Wheelie and Brains watching Star Trek and saying "This is the one where Spock goes crazy", which is some pretty nasty foreshadowing.
The man that played Buzz Aldrin was actually Buzz Aldrin.
Sentinel Prime's "rust gun" may be a reference to cosmic rust, any of the various transformers who have carried corrosion-based weaponry over the years, or simply a coincidence.
Ironhide's death is likely something of a reference to the 1986 TF movie.
Soundwave is missing the Mercedes badge on his chest during the camp scene, probably to hide his reveal later.
When the Decepticons first arrive before the garbage truck scan you see a 'con transform into a white police car while jumping to the floor, look dead center of the screen to see.
Sentinel's "helmet" is identical shape to Optimus's - Look at the sides, it gets knocked off Sentinel by Megatron at the end - Does this mean Optimus's can come off?
As Sentinel lines up to cut off Prime's head he says "There can be only one" - reference to Highlander movies.
It looks like Barricade is the one that kills Que. It happens so fast but look to the right of the screen as Que is fatally shot. It looks to be him.
The first and last transformations in the trilogy make the G1 sound.
When Sam enters the NEST base, Ratchet flicks his lights on and off to say hello.
Bruce is wearing yellow socks on the yellow floor.
The head that was uncovered on the Ark was what was going to used for Ultra Magnus before Sentinel was ultimately chosen.
When Crankcase transforms on the highway, he makes the same grunt that Bonecrusher made in TF1.
When Bumblebee saves Sam and Lennox after fighting Starscream, a train goes by, even though Chicago is almost entirely destroyed.
President Obama was mentioned in TF2 and shown in TF3, but a fake president was used in TF1, even though he somewhat resembled George Bush.
Barricade asks Bumblebee,"Remember me?" when some of the Autobots have been captured. (Not confirmed)
The plane that Sam and Mearing are on while on their way to Florida has an Autobot logo on it. This means it could be an Autobot or it could just be because it is a NEST plane.