Wish can emulate any wizard/sorcerer spell up to 8th level.
Can I wish, for example, to emulate a maximized (+3) empowered (+2) fireball? The same fireball if prepared would occupy a 8th level slot.
The 9th-level Sor/Wiz spell wish [univ] (PH 302-3) says, in part, that the spell can, "Duplicate any wizard or sorcerer spell of 8th level or lower, provided the spell is not of a school prohibited to you." The 3rd-level Sor/Wiz spell fireball [evoc] (PH 231) modified by the metamagic feats Empower Spell (PH 93) and Maximize Spell (PH 97-8) must normally be cast using an 8th-level sorcerer or wizard's spell slot, but such a modified spell remains a 3rd-level spell for all other purposes (albeit its save DC is as per a 9th-level spell if duplicated by the wish spell). (It takes the feat Heighten Spell (PH 95) to increase a spell's actual spell level.) That means wishing for an empowered, maximize fireball could be a legit and simple wish, not providing "the DM the opportunity to fulfill [the wisher's] request without fulfilling it completely" (PH 302). In short, the argument goes, a spell—even one modified by metamagic feats—remains a spell.
This is dangerous territory, though. Using the wish spell to duplicate an 8th-level spell—even a spell as silly as the 8th-level Sor/Wiz spell polar ray [evoc] (PH 262-3)—to which has been applied every metamagic feat in the game except Heighten Spell is a cause for concern.
Thus the DM may rule that because the game does not explicitly say that using the wish spell to duplicate a spell modified by metamagic is possibile—the spell description's being silent on the topic—using a wish to duplicate a metamagic-modified spell just isn't possible (perhaps citing this strip). Unless the wisher is willing to court catastrophe via a DM's deviousness and cast the wish spell to duplicate a spell modified by metamagic as a "greater effect" wish, a DM could rule that a wish used to duplicate a spell simply and only duplicates the basic, unmodified spell. (In which case, please, just wish for a spell superior to fireball—there are tons!)
Alternatively, a DM seeking a middle ground—wanting to give creatures options but worried about his campaign—may allow the wish spell to duplicate spells modified by metamagic but apply specific limits. For example, a DM fretting that PCs might abuse the privilege of being able to employ wish to duplicate spells modified by metamagic could make a house rule like A wish spell can duplicate a sorcerer or wizard spell that's modified by one or more metamagic feat's benefits if both the ensuing duplicated spell would occupy an 8th-level or lower wizard's spell slot (or expend an 8th-level sorcerer's spell slot) and the spell is not in one of the caster's prohibited schools then make similar house rules for other lower-level duplicated spell.
Using metamagic does not actually change the level of the spell. Nor is it considered a new type of spell in its own right. A maximized empowered fireball is still a 3rd level spell despite being prepared as an 8th level spell or using an 8th level spell slot. The rules for Metamagic feats explicitly point this out.
Spells modified by a metamagic feat use a spell slot higher than normal. This does not change the level of the spell, so the DC for saving throws against it does not go up.
Though wish can duplicate the effects of lower level spells, it still functions as a 9th level spell. The text reinforces this by pointing out that the spell effect uses saving throw DCs for 9th level spells.
Duplicate any wizard or sorcerer spell of 8th level or lower, provided the spell is not of a school prohibited to you. ... Duplicated spells allow saves and spell resistance as normal (but save DCs are for 9th-level spells).
Metamagic feats also have highly restrictive rules about when and how you can apply them to spells. You cannot apply Metamagic effects unless the rules or another ability specifically say you can.
Thus, you cannot use wish to duplicate the effects of a spell with Metamagic feats applied because...
This use of wish specifically says you cast an 8th level spell (or lower)
The resulting wish is a 9th level spell
Fireball is a 3rd level spell
Neither Metamagic feats nor wish specifically allow you to change the duplicated spell's actual level through metamagic feats
The wish spell points out that you can create other effects with DM discretion and implies you can create an effect that's on par with the other options. So, you can ask your DM to have wish duplicate the effects of a hypothetical new wizard/sorcerer spell that has the same effects as a maximized empowered fireball.
You may try to use a wish to produce greater effects than these, but doing so is dangerous. (The wish may pervert your intent into a literal but undesirable fulfillment or only a partial fulfillment.)
At a first glance, I would say No, it can't, but let me explain why.
Duplicated spells allow saves and spell resistance as normal (but save DCs are for 9th-level spells).
Spells duplicated under wish act as if they were Heightened to 9th level, as such, you can no longer apply metamagic feats as that would increase the spell level above 9th.
There are contradictions on the spell, though. Like saying that "Duplicated spells allow saves and spell resistance as normal" but what is normal here? The spell, or wish? Because for saves, Wish tells you to "see text", while for saves Wish tells you "Yes".
Casting Time: 1 standard action Range: See text Target, Effect, or Area: See text Duration: See text Saving Throw: See text Spell Resistance: Yes
The spell's casting time is a Standard Action regardless of the spell duplicated, meaning that a quickened magic missiles would still be cast as a standard action. But that also means that any spell with an Immediate casting time would also require a standard action, and spells with longer casting time (instant clones and slaves) would be cast much faster.
For saving throws, it is clear that it should allow a saving throw if the spell duplicated allows a saving throw. But for spell resistance its ambiguous, it says "Yes" but also says it works like "normal". What is normal? One GM could say that all spells duplicated are affected by spell resistance, even those who normally are not (like orb spells). While another could say that it depends on the spell being duplicated because the spell effect says they work as "normal".
Also, the spell's effect says that wish produces a certain effect, which then explains that it can duplicate the effects of those spells.
A wish can produce any one of the following effects.
This all leads me to believe that the spell being cast is only Wish, and not Wish plus Fireball or Fireball. So if you have to counterspell it, you have to counterspell a 9th level spell, saves DC are against a 9th level spell, and Spell Immunity does not apply against our Wish-Fireball.
Though the spell duplicates the effects of another, you are not in fact casting that spell. I would even say that a spell focus (evocation) does not increase the DC of our Wish-Fireball. The spell being cast is still a spell from the Universal school producing effects similar to those of an Evocation school.
However, this also means that metamagic reducers, like Arcane Thesis (PHB II), could be applied to Wish and affect all spell effects duplicated by Wish.