Let's assume this is max power Magus. That is, the version of him in the Ocean Palace right before he gets owned.
Vs. Nibelheim Sephiroth - Magus wins. In this form, Sephiroth is just another mortal, albeit one with great strength from Jenova cells. Yes, he torched the town. But he had a mastered fire materia to do it with, it wasn't all his power. Whereas Magus could have atomized the place with dark matter. Just too great a power disparity.
Vs. FFVII Main Story Sephiroth - Once again, a huge power difference. But in this case, Sephy does the victory dance. Why? Jenova, by itself, is a Lavos-level opponent. It survived the Northern Crater impact. It messed with the lifestream and people's minds. It massacred most of the Cetra race, which could draw upon the planet's power to an extreme level. And Sephiroth made it his slave. Yeah, our favorite warlock is screwed.
Vs. AC Sephiroth - ...umm, I haven't seen AC. This shames me as a devoted. Can someone else take this one?