Origin of the term
"Beast Wars: Transformers" (1996-1999)
Protoforms are usually already imbued with a spark (self-awareness, life essence) before being placed into a stasis pod; those without a spark are referred to as "blanks". During the Axalon's journey, the Quantum Wave possibly destroyed these sparks while leaving the bodies intact. It is also possible that these blanks were intended to be used as spare bodies for the crew in case their own were damaged or destroyed.
Stasis pods are also rather delicate, and the slightest damage can erase the protoform's memories. As a result, of the protoforms activated during the Beast Wars, only Rampage (and Packrat in the comic series) has any memory of life before going into stasis. It is likely that the others also had lives on Cybertron, as all Transformers who emerge from the pods seem more mature than Cheetor.
It is unknown in what era of Cybertronian history that protoform technology became available. In the Dreamwave comics, protoforms exist in the Micromasters series, which is set on Cybertron after the Ark and Nemesis were launched and lost in space.
It was implied in the television series and Wreckers comic book that some of the protoforms were criminals shipped off planet. This was the case with Packrat (a master thief) and Protoform X (aka Rampage, a serial killer).
In the IDW Publications mini-series, Beast Wars: The Gathering, the Predacon Magmatron and his troops arrived on Earth on a mission to follow up on the failure of Ravage. Magmatron had his own agenda to convert many of the unused protoforms in stasis pods into Predacon soldiers under his command, but the Maximal under cover agent Razorbeast sabotaged the plan, resulting in many of the protoforms emerging as Maximals. Magmatron also recovered the remains of Ravage and used a blank protoform to bring him back as a Transmetal.
"Transformers: Animated" (2009)
In this series Optimus Prime states that, "Protoforms are the building blocks for all life on Cybertron", much like the liquid metal protoforms of Beast Wars though can assume a physical blank form when not in use. They were placed in the care of Yoketron, who trained Prowl to eventually take his place should the time come. However, a fallen student of his named Lockdown led a raid of Decepticons, stealing almost all the protoforms and damaging Yoketron. Prowl, returning from a quest to find himself, used the remaining protoform and transferred his master's spark into it. Despite this, Yoketron forced himself offline. The stolen protoforms ended up in Megatron's warship, utilized by Starscream to create his clones before Megatron uses three to build his own three clones of Omega Supreme. The remaining protoforms were later taken back to Cybertron after Megatron's permanent capture.
Though a series of events yet to be revealed, one child-like protoform mysteriously ended up in the lab of Professor Isaac Sumdac. Touching the protoform while examining it, Prof Sumdac unintentionally encoded his genetic makeup into it before being knocked unconscious by the residual energy. As a result, the protoform became Sari Sumdac with no knowledge of her origins or nature as a techno-organic being.
In the 2007 live-action film Transformers, Autobots en route to Earth change their alternate modes into structures called space travel pods by the movie creators in the additional material contained in disc 2 of the DVD release, (a possible homage to the stasis pods plot device from Beast Wars) and enter the planet's atmosphere in the same way as a meteor. Thereafter, the Cybertronians change to a humanoid shaped endoskeleton structure known as Protoform by fans.
Once they arrive, Cybertronians in protoform state will transform into an equally detailed yet generic & undefined robot mode to allow them more stable ground mobility in order to search for an adaptable disguised form (aka vehicle mode); upon which scanning and replication are initiated and completed within seconds, giving them their now-unique physical characteristics. These near-identical transformable skeleton-like forms are referred to by fans as protoforms due to their generally similar appearance and function to the Beast Wars versions, though they are not specifically named such in the film. Also, a protoform retains the same mass as the final appearance of a Cybertronian with a chosen vehicle mode after scanning & replication are complete, so one protoform can be larger and/or smaller than another. Whether-or-not a protoform has [usable] weapons is not shown or mentioned in the film. In the Transformers: Movie Prequel book, protoforms are the base forms for all transformers on Cybertron, hence their skeletal look; all armor, weapons, sensors, transformation, etc. are integrated into this later when landfall is made. (Bumblebee is portrayed on Cybertron as a protoform and later in the book Starscream, Barricade, and Blackout are seen as protoforms on Mars). It should also be noted that a Transformer can apparently turn into a protoform as much as it needs to. Bumblebee first landed on Mars and then went to Earth after finding a Mars rover, evidencing the theory.
Also in the additional material of the DVD, director Michael Bay states that he wanted the Transformers to arrive to Earth in their protoform, calling them endoskeleton/underskin, to avoid logic contradictions found in the original Generation 1 animated series, such as some Autobot characters carrying pieces of human-created technology, like truck and car pieces, while they were on their homeplanet Cybertron, clearly an alien environment. Bay states that while that was done in the cartoon for the sake of easy animation, it wouldn't fit well in a movie he envisioned to be serious, and wouldn't help to make the film credible to audiences not familiar with the Transformers universe.
Production designer Jeff Mann goes as far to explain in the extra features of the DVD, that the technology of the Transformers machine replication is beyond human understanding, based on a nano-molecular process, being each one of their molecules and each one of their cells a machine unto itself, which explains how Cybertronians in protoform state are able to adopt the form of any machine or vehicle of the same mass, replicating materials such as rubber (wheels), glass (windshields), fiberglass, and the like.
Much unlike those in Beast Wars, protoforms in the live-action film are shown to be extremely tough and durable, obviously withstanding the atmospheric reentry and hard landing as they arrive on Earth, as said by the Transformers Movie Guide; whereas in Beast Wars, protoforms (see above) are portrayed as fragile and delicate.
The Nintendo DS versions of the video games based on the two live-action Transformers movies have the player controlling a new character, first shown as a protoform. In the game based on Transformers: Revenge of the Fallen, Optimus Prime uses this terminology.
Transformers: Revenge of the Fallen (2009)
In the second movie, several protoforms arrived on Egypt. One of the protoforms scanned a Buffalo H. In other scene, Megatron arrived on a meteor and are shown baby protoforms (hatchlings).