The Ultimate Program was only seen in the Anime and not in the Video Games series.
Known Possessors of the Program
Each Navi that had the Ultimate Program had a unique ability displayed multiple times in the anime that allowed them to either win battles, become stronger, or have special unique attributes.
The Ultimate Program enabled MegaMan to make use of the Style Change in the beginning, obtaining HeatGuts, WoodShield, ElecTeam, and AquaCustom Style. When the bug that was inside Bass entered MegaMan, his Ultimate Program invoked a Style Change in an attempt to repair itself, the Bug Style. His Program was powerful enough to overpower the Grave Virus Beast and ProtoMan's Ultimate Programs, absorbing the entire Net, before restoring everything after Lan got through to MegaMan.
In Axess, MegaMan had lost his ability to Style Change due to having performed a Cross Fusion with Lan, but in so, MegaMan obtained a new power, called the Double Soul, instead. With it, MegaMan was able to perform a much higher level version of ElecTeam Style, where MegaMan could take another Navi's strengths and abilities into his own, and even transform into form similar to the original Navi. It was shown that Double Soul was even possible during Cross Fusion, but the act consumed incredible amounts of energy from Lan, that rendered him completely incapcitated. It is highly possible that MegaMan's Ultimate Program seemed to take in the energies of the other Navis while Lan was incapacitated and then enable a Full Synchro, allowing him to easily defeat a giant Cross Fused Regal.
Later on in Stream, Bass attempted to absorb MegaMan's Ultimate Program to become a super powerful being that could face Duo, but was thwarted with ProtoMan's intervention. When Bass had succeeded in absorbing MegaMan's Ultimate Program, he couldn't control it, with resulted in MegaMan activating the Double Soul instead and becoming Bass Cross MegaMan, the resulting power being phenomenal that Bass Cross MegaMan managed to easily defeat Nebula Grey, though the amount of power was too great for their body to handle, and thus they ended up becoming exhausted into collapsing, and later defusing.
It is likely that MegaMan's ability to merge with Trill to enter a Gregar and Falzar Beast Out was also a result of MegaMan's Ultimate Program. This was taken even further when in Cross Fusion with Lan when heading to face the Super Cybeast Grezar, where Lan had managed to combine both Gregar and Falzar forms into the his Cross Fused state.
Later on, MegaMan could access the Beast forms at will from turning the power of Gregar and Falzar in him into Battle Chips. He also obtained the ability to Cross other Navis as well and even merge it with his Beast forms.
When Bass was born from PharaohMan's remaining data, he lacked the Ultimate Program, as it was used to create the Grave Virus Beast. For that, Bass had an instinct to absorb data and bugs into himself, and eventually learned of his origins which led him to attempt to merge with the Grave Virus Beast, but he had been absorbed instead. After MegaMan had successfully restored the Net and deleted the Grave Virus Beast, Bass had obtained his Ultimate Program again, becoming whole once more, though it is speculated that Bass hadn't regained all the powers he had as PharaohMan.
Bass' Ultimate Program seems to be similar to his game version's Get Ability Program, as Bass attempted to absorb MegaMan and ProtoMan, though he failed to absorb either. He had absorbed MegaMan when MegaMan offered it to Bass to stop Nebula Grey, though Bass couldn't handle MegaMan's Ultimate Program and nearly self-destructed, forcing MegaMan to use Double Soul instead, forming Bass Cross MegaMan. However, the combination of the two's Ultimate Programs was immeasurably powerful, easily defeating Nebula without so much as a scratch on Bass Cross MegaMan. After separating and being absorbed into an abyss, Bass managed to absorb the remaining power of Nebula Gray to become much more powerful that he could face Slur, who had easily defeated Bass before. The result allowed Bass to easily defeat Slur, deleting the extraterrestrial Navi in the end.
Not much has been shown of ProtoMan's Ultimate Program, if there had been any special qualities, but ProtoMan has shown a very powerful range of skills, and was able to defeat multiple foes at once, along with being able to handle himself in many situations, which allowed him to fight MegaMan on even ground multiple times, and even overpower him.
Iris' Ultimate Program wasn't used for battle, but it is likely that her Ultimate Program is what allowed her to enter the human world and the Net at will, as well as taming MegaMan's Beast Out states, and even helping a proper merge with Trill to enable MegaMan to control his Beast Out.
It was created from PharaohMan's Ultimate Program, and it allowed the beast to grow stronger with every Navi and data that it could absorb. It allowed the beast to easily take on the most powerful of attacks and break through powerful firewalls that was used to contain it. It was only Bass and MegaMan Bug Style that could stand up to the beast, though Bass ended up being absorbed himself when he attempted to absorb the Grave Virus Beast. When it attempted to absorb MegaMan, it was ultimately absorbed and deleted, though Bass had reclaimed his Ultimate Program by then.
Though his Ultimate Program was used in the Grave Virus Beast and Bass, PharaohMan didn't display any unique abilities for battle, but instead was a very powerful Navi that could easily take over the Net by controlling the flow of data. Even an army of BomberMan.EXE and StoneMan.EXE couldn't defeat him, much less hurt him, and he easily destroyed the army. Despite how the power in SciLabs was shut down, PharaohMan successfully rebooted the entire system, despite how it shouldn't have been possible. It was only when MegaMan and ProtoMan had used a Double Program Advance on him that PharaohMan was wounded, which led to his capture, and eventually him self-destructing to prevent himself from being used by a human.