1) Movie verse: Instead of Optimus and the other Autobots arriving on Earth its Elita One and her team.
2) Movie verse/Pacific Rim crossover: Instead of Kaiju its Decepticons. The humans get the Jaeger idea from a frozen Megatron. Now they fight Decepticons using Jaegers. Eventually the Autobots come to Earth to help.
3) First Aid/Slingshot
4) Red Alert/Beachcomber
5) TFP: Raf gets eye contacts
6) G1: "I miss Cybertron. We had ships to get us places."
7) In recharge the Aerialbots dream of who they were in their past life.
8) The war is over. A neutral decides to be an Autobot to impress bots and a former Autobot confronts them.
9) Spike and Bumblebee help a human change their vehicle's tire.
10) Autobot: "Hey we made the news again."
"Car Thieves Tried to Steal An Autobot"
11) "Buzz off, Bumblebee!"
12) "Take a hike, Hound!"
13) "Hide! Ironhide is coming!"
14) "Hoist me up."
15) Grimlock steals Sideswipe's jet pack and takes it for a spin. Literally. He goes in circles.
A) "How you work this thing!"
16) "How can you mistake Optimus Prime for someone else?!"
17) "They should make worse role model awards. I know several bots who deserves the award."
18) G1: Wheeljack accidentally creates two Optimus Prime's.
19) TFP: Bulkhead and Miko fall in a mud hole and are covered from head to toe in mud. Humans see them and think they are Mud Monsters. They think Bulkhead is a mother because there is mud monster child beside it.
20) Beast Wars/Prime crossover: Inferno comes through the portal and calls Megatron his Queen.
21) The humans keep saying they see a mirage in the desert and Mirage with the rest of the Autobots are confused when they are not calling his name.
22) He turned the corner gleefully knowing he was going to win and walked into Jazz's gun pointed at him.
"Looks like I win, Bluestreak."
23) The Decepticons create a drone, paint it Elita One's colors and pretend to hold her hostage.
24) An Earthquake shakes the Ark and a crack opens up in the floor causing a little lava to spill into the Ark.
23) "Knock, knock. Honey I'm home." Announced an Autobot at the entrance of the Ark.
24) G1: The medics watch MASH.
25) The Autobots learn about sleep walking when one of the humans do it and doesn't remember doing it even though Red Alert has footage of it.
26) Optimus can see dead bots because he wears the matrix. A ghost helps him and his soldiers escape unharmed from an ambush.
27) G1: The US builds an Optimus Prime monument.
28) The Aerialbots are shocked when Gears saves Spike from falling in midair. (I read on wiki Gears can release controlled bursts of compressed air from his feet, launching himself to altitudes over 100,000 feet, and floating back down.)
29) The Autobots look for wounded in a sandstorm.