The spell Prismatic Sphere, references Prismatic Wall, which says:
The wall can be destroyed, color by color, in consecutive order, by casting the specified spells on the wall; however, the first color must be brought down before the second can be affected, and so on. A rod of cancellation or a mage's disjunction spell destroys a prismatic wall, but an antimagic field fails to penetrate it. Dispel magic and greater dispel magic can only be used on the wall once all the other colors have been destroyed. Spell Resistance is effective against a prismatic wall, but the caster level check must be repeated for each color present.
So clearly a prismatic sphere is destroyed. I don't have such a clear source to say that other spells are out right destroyed, but that's just what Mage's Disjunction does. It only references Dispel Magic to tell you what happens when the spell happens.
Edit:
You can use dispel magic to end one ongoing spell that has been cast on a creature or object, to temporarily suppress the magical abilities of a magic item, or to counter another spellcaster's spell.A dispelled spell ends as if its duration had expired. Some spells, as detailed in their descriptions, can't be defeated by dispel magic.
I think these are the relevant parts from Dispel Magic that apply to Mage's Disjunction. I agree that there would be no reason to use Mage's Disjunction if it worked exactly the same as Dispel Magic because you'd be wasting the high level spell slot. Mage's Disjunction just automatically dispels every spell in it's radius providing that it is capable of being dispelled. To be clear, Mage's Disjunction does not require any check to dispel spells.
As above, I have a few questions that have been an argument between my GM and me. He believes that this spell, as it says "(ending the effect as a dispel magic spell does)" with the keyword being DISPEL MAGIC, requires me to make a caster level check to end every spell effect. I, however, believe it isn't required - otherwise why in the high heavens would i use a level 9 spell to do the same thing that a dispel (or greater dispel for that effect) would achieve?
Because, Greater Dispel Magic can only affect a 20' radius area with an area dispel, while Disjunction affects a 40' area.
And, the area burst from a Greater Dispel Magic has no effect on magic items, just spells. The area burst from Mage's Disjunction not only affects spells, but magic items as well.
Area Dispel: When greater dispel magic is used in this way, the spell affects everything within a 20-foot-radius burst. Roll one dispel check and apply that check to each creature in the area, as if targeted by dispel magic. For each object within the area that is the target of one or more spells, apply the dispel check as with creatures. Magic items are not affected by an area dispel.
Also, as the area dispel option of a Greater Dispel Magic says it works like you had targeted a normal Dispel Magic on the creatures in the burst, then it can only dispel one spell on each those creatures. Mage's Disjunction specifically says it affects all magical spells in the area, so multiple spells could be dispelled from each creature inside the area.
Think of Mage's Disjunction as an Even Greater Dispel Magic spell.
It seems pretty clear that you don't have to make a caster check to end the effect, it is just ended.
As far as the occupant of the sphere, he was inside the radius of the disjunction, therefore is affected by it. I can see other interpretations, but I think of it like the prismatic sphere is like wet tissue paper when up against the magic destroying power of mages disjunction. It offers no protection to it's occupant.
All you need to know is this "All magical effects and magic items within the radius of the spell, except for those that you carry or touch, are disjoined."
It gives the special cases such as magic items, artifacts, and Anti-Magic. It is NOT Disple Magic or a greater form of it. It simply mentions in passing that the effects are gone like what happens when you dispel something.
Prismatic Sphere - Gone!