I kind of think FFVII is the Magnum Opus of FF. Not because it's the best or anything, but it remains by far the most popular and for many it's the first title that comes to mind when they hear the name of the series. I'd call III the Parvum Opus because it has a huge cult following, but from the mainstream FF fan perspective, and an even larger perspective, it's probably the most overlooked title (not helping matters is the fact that its name was originally taken by a far more popular installment).

(Also, I wanna know what Choco Boy is smoking )

Anyway, another huge series that comes to mind is, of course, MegaTen. From the main series, I think Nocturne might be the Magnum Opus, because even if IV refined many of the main series' elements, Nocturne is still what many people consider the best and most fulfilling one, being the only fully 3D one and being the darkest. Strange Journey is the Parvum Opus as it really seems to be the most forgotten and the least revolutionary, despite being my favorite main title.

Either Persona 3 or 4 are the Magnum Opus of that series. Heck, Id collectively call both that, as one really made the series alive again (and Atlus relevant), while the other is one of the biggest critical darlings I've seen. Persona 1 is obviously the Parvum.

The Sims 3 is most definitely the Magnum Opus in that series, especially with the Sims 4 not being the step forward that was expected, instead being kinda a step sideways, if that makes sense. The Sims 1 is the Parvum Opus - for all the fun we had playing it when it came out, it's most certainly the least robust. But until that happened, it was certainly Maxis' Magnum Opus, which is interesting.

Pokemon X and Y are the Magnum Opus of Pokemon, bringing many fans back and making the largest amount of Pokemon available. Black and White are the P.O. - despite being overall superior to XY, IMO, with their story and being just different from the rest of the series, seems to be the one most overlooked, with gen1 having that nostalgic edge, gen2 being considered the best by many, gen3 having a modern remake and people wanting a gen4 remake now. No one seems to remember the enhancements gen5 introduced that allowed XY to be what they are.

That's all the series I can think of now. I'll probably come back with some more later.