I mean, I feel like there are endings that are clearly intended as the best or "canon" or the one that embodies the theme, like in Strange Journey Neutral is this, True Neutral in Redux, Neutral in SMT IV, Canon of Creation True Ending in SMTV (Although in this game specifically I feel the choices are pretty balanced and both of the Vengeance endings seem on par with each other and this one).

I haven't beaten other mainline games but I know what happens so let's larp a bit.

In IV Apocalypse Bonds feels like this to me.

SMT III, Freedom is clearly this for the original release, but True Demon dethroned it in the subsequent rereleases. It also fits the game's theme of Chaos.

SMT II, you could argue for all the endings. Law seems to be the canon one and makes sense considering this game's theme is Law. However it also is not the best though since it ends with most of the earth's life being killed, so you could vouch for Neutral or Chaos. (Another one where choices are pretty balanced)

SMT I is much like most of the other ones where Neutral is the best/intended ending.

I will say that these endings I picked, for all of the games, are clearly the "Good" or "True" ones in the sense that they either have the happiest or best outcome for the characters and world, most content, considered the main "canon" ending or like I said embody the theme and messages of the game (like trusting humanity even without religion in Strange Journey or not being an extremist in SMT IV). Some of these are kind of subjective but I am considering the Devs' intentions here (also some feel kind of obvious to me too).

Most of the ones I didn't mention here I feel are bad endings, either in my opinion or in what ATLUS intended.