(Subject to disagreement, please be bold in editing)

The canon of PRPG comprises, at least, part of the MLP:FiM cartoon, [[PRPG1]], [[PRPG2]], [[PRPG3]], and their canonical one-offs.

The PRPG universe visibly diverges from the MLP:FiM canon; specifically, it includes all season 1 and 2 episodes except for "A Canterlot Wedding". (The game began in 2012 and obviously conflicts would inevitably arise as the show continued, in an uncontrolled way if a departure point had not been set.) Many elements (including most notably changelings) from subsequent episodes have been individually canonized or referenced, however, and PRPG2 especially includes many references to G1 MLP content. As a general rule of thumb, 'world-building' items from MLP:FiM are likely canonical, but specific events are less likely to be.

PRPG1 and PRPG2 share a common universe until at least sometime after the end of PRPG1. At this point, there is the [[PRPG1 Epilogue|so-called good ending]] of PRPG1, which has the Golden Age changeling society coming to live with ponies openly, and becoming incredibly powerful in a symbiotic relationship with ponies. Conversely, in the backstory of PRPG2, this did not happen, and En-Netsusep invaded to extirpate changelings, causing the [[Catastrophe]] instead. So, PRPG2 and any PRPG2 one-offs after this point of divergence are not canonical to PRPG1, but the ones set in the past relative to PRPG1 are (e.g. the Eldritch Lore cycle excluding the infamous [[Special Agent Shiny Buttons]] one-off, which is not canonical because it didn't end like it did in the backstory.)

There are other possible viewpoints on the canonicity relationship, however. In PRPG1, an [[Eldritch Lore|accomplished future-diviner]] saw the Isle of Yore in its post-catastrophic state, and the party also saw a vision of what was implied to be that future. Based on how divination works (including in PRPG1), this would tend to imply that it is in fact the ''PRPG1 Epilogue'' that represents the "alternative" universe. (There are other explanations as well, albeit somewhat contrived - the divination might not have been true divination, for example, or people in-universe might, knowing of what she saw, have staged events such that the timeline could be fixed on a false disaster instead of a real one, if they had read about the divination in [[Silver Journal|Eldritch's journal.]])

PRPG1 and PRPG2 are canonical to PRPG3. Unlike PRPG1 and PRPG2, where the major settings were geographically distant, PRPG3 and PRPG2 both have many sessions taking place on the [[Isle of Yore]].

The canonical relationship of Ponecia to PRPG is not entirely clear. It shares a number of world-building decisions with the PRPG games, but does not have a clear chronological relationship to PRPG1 or 2 beyond being in their future. 

The HICU-RPG gaming group has had a number of other MLP-themed one-offs or episodic campaigns, especially [[Matt's Pony Continuity]] which has its own independent canon, and various pony-themed one-offs that are alternate universes using PRPG characters, or have no relationship to any other one-off.

Obviously, outside of the game itself where what the GM thinks is most salient, what is canonical is ultimately up to the individual reader.