A Super Mode is an auxiliary transformation some Cybertronians possess that is used sparingly, perhaps due to a higher energy consumption. This transformation often involves combining with unused portions of their alternate mode and bringing normally concealed weapons systems online. This form is often a variation on the robot mode, but there are many who possess vehicular or other Super Modes. In some continuities, it is referred to as a Battle Mode, Brute Mode, Hyper Mode or Ultra Mode. A robot-mode super mode is, amazingly enough, often called a Super Robot.
One might easily consider Ultra Magnus one of the earliest examples of a Super Mode, due to his toy combining with his trailer to form a Super Robot. However, due to the recognition factor and possible confusion with Optimus Prime, he was never depicted in his primary robot mode. This made his Super Mode his de facto normal mode.
This was later superseded by Optimus Prime's upgrade into a Powermaster, by which he acquired a canonical Super Mode. Of course, the series ended immediately thereafter.
Masterforce (Japan Only)
Ginrai, much like his American Powermaster counterpart, possessed both a robot mode and a Super Robot mode from combining with his trailer. As well, he could combine this powerful mode with the Godbomber drone to form a still larger and shinier "God Ginrai" mode. Though Godbomber had no counterpart in the English-language fiction, the rerelease of Powermaster Optimus Prime included the mold improvements featured in Ginrai as well as the Godbomber figure, renamed Apex Bomber, who formed Prime's "Apex Armor."
Victory (Japan Only)
Star Saber was a double Brainmaster, starting as a small robot known as Yukio, combining into a larger robot named Saber, and finally forming an even larger robot known as Star Saber (natch). This robot could then be enhanced further by combining with Victory Leo to form Victory Saber.
Beast Wars II (Japan Only)
In the Beast Wars II movie "Lio Convoy in Imminent Danger", the characters Lio Convoy and Optimus Primal (called Convoy) used the power of their Matrixes to transform into Flash Lio Convoy and Burning Convoy in order to defeat the out of control and overwhelmingly powerful Majin Zarak.
Lio Convoy also possessed the ability to merge with his doppelganger Lio Junior to become what was known as the "Legendary Warrior". Interestingly enough, the "Legendary Warrior" was merely Lio Convoy colored completely green, but he was immensely powerful and managed to defeat the Angolmois powered Galvatron.
Robots in Disguise
Optimus Prime initially had a smaller robot mode composed of just his vehicle mode cab, which could then combine with pieces of his "trailer" to form his larger, more powerful Battle Mode (this mode was called Super Fire Convoy). Later on, he and Ultra Magnus could combine to form the Super Robot Omega Prime. Neither was the dominant personality in this fusion, much to Magnus's disappointment.
Also, the three Autobot Brothers Side Burn, Prowl, and X-Brawn each possess the ability to Power Up into a Supercharged form, after receiving a power boost from Ultra Magnus when the Matrix was being shared between him and Prime.
Optimus Prime could combine with his trailer to form his Super Mode. He could also combine with Jetfire to become Jet Optimus. Both of these Super Modes could be further enhanced by mounting Overload on their shoulders.
Optimus Prime could combine with the four drone vehicles stored in his trailer, with each forming an arm or a leg Scramble City style, leading to a wide variety of Super Robot modes. Prime could be further enhanced by combining with Wing Saber to form either his heavily armed "Fight Mode" or the more maneuverable "Flight Mode". Prime could also combine with Omega Supreme to form "Optimus Supreme".
There are also the "Hyper Modes" assumed by the Decepticons. Aside from the smaller Terrorcon, and Decepticon combiners, every large Decepticon has a hyper mode. Sometimes, it is just a minor repositioning of parts, as for Slugslinger, but in many cases, it reveals a hidden weapon or accessories like Sharkticon's side cannons or Snow Cat's skis. In the case of Scorponok, Shockblast, and Six Shot, their third mode (scorpion or satellite) acts the vehicle mode's hyper mode, the vehicle mode being a plane or a laser tank.
In Transformers Cybertron, Optimus Prime transforms into Super Mode. Most of his trailer goes onto his back while two leg pieces connect to the blue part of his legs and his mouthplate comes over his face. Optimus Prime goes into Super Mode when fighting in battle against anybody vaguely threatening.
Conversely, Megatron could form the "Dark Claw Mode' with Nemesis Breaker.
IDW G1 Comics
Nova Prime possessed a Super Robot mode formed by combining with his vehicle mode's trailer. This form also granted him wings and thus the power of flight.
Thunderwing revealed that not only were his robot and jet modes enhanced by the Pretender process, but he also possessed an extremely powerful tertiary "Ultra Mode." However this form drew heavily from the reserves of Ore-13 that were powering him, causing the enhanced energon variant to go critical and burn him out from the inside.