Canon, in terms of videogames, is what actually happened in the storyline. Changes in what is considered canonical (when they occur) are often a result of earlier translation errors, other developers creating a story without consideration for the established storyline of the series, or significant mid-series overall-storyline changes.
For example, Castlevania Legends for the Gameboy is no longer canon. It interfered with the plot of Castlevania 3, made Alucard Trevor's father, gave no explanation as to why Dracula would be resurrected only a few years afterward and how he could start taking over Europe after having been killed so recently, and a whole slew of other problems. When Koji Igarashi got complete creative control over the series, he said "Wow, this storyline is a mess, let's clean it up," and removed Castlevania Legends from canon. He retconned it into a side-story or a what-if scenario.
Another example of a game going from canon to not-canon would be Resident Evil for the gameboy. This game took place on a cruise ship and starred Leon Kennedy from Resident Evil 2. At the end of this game, Leon is infected with some sort of virus.
In the original conceptions of RE4 (well, ONE of the original conceptions), they were going to continue this storyline and start off with Leon infected by some kind of virus that would cause hallucinations. When they revamped RE4 and scrapped the early build, and started making the game we now have, they ditched that storyline as well. Leon isn't infected with any virus, and the gameboy RE "never happened."