Sure you can, as long as you meet the prestige class’s prerequisites. The Commoner class does not have any special rules about its advancement, it’s just a particularly weak base class.
It’s actually the easiest way to enter the Survivor prestige class (Savage Species), which requires that one’s highest base save bonus be lower than one’s character level. In a similar case, the Adept is the easiest way to enter the Hexer prestige class (Masters of the Wild), since it requires lightning bolt as a divine spell, and neither clerics nor druids get it, nor is it found on any Domain (amazingly).
I would comment that a common way to handle games where you start as Commoners is to have you “trade in” Commoner levels for PC-class levels, to avoid you taking pretty serious hits to your abilities relative to your nominal ECL. This is a non-issue if your DM knows how to compensate, but it might be worth mentioning as an idea to your DM.
You usually need to take 1 level in the base class first
SRD > Special Abilities > Spells
Sometimes a creature can cast arcane or divine spells just as a member of a spellcasting class can. [...] A spellcasting creature is not actually a member of a class unless its entry says so
Since prestige classes (almost always) require you to choose a class (that you already have levels in), and in most cases your innate spellcasting explicitly does not count as having any levels in the class you cast spells as, you cannot expect a prestige class to help here.
However!
SRD > Improving Monsters > Associated Class Levels
A spellcasting class is an associated class for a creature that already has the ability to cast spells as a character of the class in question, since the monster’s levels in the spellcasting class stack with its innate spellcasting ability.
(emphasis mine)
Thus, when you take a level of wizard as a marrutact (or a level of sorcerer as a dragonspawn or a level of bard as a gloura), this stacks with (improves) your innate spellcasting, and means you have membership in that class for the purposes of choosing it with a prestige class. Since both the innate spellcasting and the prestige class levels stack with the base class, your total “effective” spellcasting level includes all three sources.
Note that for creatures like angels that cast as clerics and have domains, real-class-membership has further benefit:
SRD > Special Abilities > Spells
A creature with access to cleric spells must prepare them in the normal manner and receives domain spells if noted, but it does not receive domain granted powers unless it has at least one level in the cleric class.
Many thanks to @Forrestfire and @Taveena for helping me track down these rules.
But there really isn’t a great reason to require the 1-level dip in the base class
Ultimately, I’ve never met a DM who actually required that one level, and refused to allow the prestige class to just work. It seems appropriate and I’m dubious that there are any cases where it is broken to do so (at least, assuming the base creature wasn’t already broken on its own; there are definitely cases of that – Black Ethergaunt, I am looking at you).
Best Answer
There's No Limit to the Number of Prestige Classes a Character Can Take...
...That is, if the character qualifies for the prestige classes. A character who qualifies for multiple prestige classes can take levels in multiple prestige classes. In fact, it's often a good idea to do exactly that so you end up playing the kind of character you want. The DM can limit which prestige classes are available in his campaign, however, so asking first is always a good idea.
It's Just Powered, Not Overpowered
Characters get things from prestige classes, but as some base classes get almost nothing for staying in their base classes, that's not a big deal. Further, meeting requirements can be challenging for the more intense prestige classes, sucking up a lot of resources that can be put toward things a character might rather do or be good at, and classes that gain high-level class features (e.g. druid) will miss those when taking a prestige class. A prestige classes is a trade-off--often a very good trade-off but a trade-off nonetheless.
O, and just to be clear: I'm not saying there aren't crazy powerful prestige classes... because there totally are crazy powerful prestige classes. Instead, I'm saying the idea of taking multiple prestige classes isn't, in itself, unbalanced.