This syntax, where subscriber[] automatically makes subscriber into a list of multiple values, is not a feature of .ini files in general, nor of ConfigParser; it's a feature of Zend_Config_Ini.
In Python, a ConfigParser ini file creates a dict mapping each key to its value. If you have more than one value, it will just override previous values. The magic [] suffix means nothing.
However, the ConfigParser constructor lets you specify a custom dictionary type or factory, in place of the default OrderedDict.
One simple solution would be to use a defaultdict(list) (or an OrderedDefaultDict, which there are recipes for in the docs) for the underlying storage, have __setitem__(self, key, value) do self.dd[key].append(value), and delegate everything else normally. (Or, if you prefer, inherit from defaultdict, override the constructor to pass list to the super, and then just don't override anything but __setitem__.) That will make all of your values into lists.
You could even do something hacky where a value that's only seen once is a single value, but if you see the same name again it becomes a list. I think that would be a terrible idea (do you really want to check the type of config.get('smtp', 'subscriber[]') to decide whether or not you want to iterate over it?), but if you want to, How to ConfigParse a file keeping multiple values for identical keys? shows how.
However, it's not at all hard to reproduce the exact magic you're looking for, where all keys ending in [] are lists (whether they appear once or multiple times), and everything else works like normal (keeps only the last value if it appears multiple times). Something like this:
class MultiDict(collections.OrderedDict):
def __setitem__(self, key, value):
if key.endswith('[]'):
super(MultiDict, self).setdefault(key, []).append(value)
else:
super(MultiDict, self).__setitem__(key, value)
This obviously won't provide all of the extended features that Zend_Config_Ini adds on top of normal .ini files. For example, [group : subgroup : subsub] won't have any special meaning as a group name, nor will key.subkey.subsub as a key name. PHP values TRUE, FALSE, yes, no, and NULL won't get converted to Python values True, False, True, False, and None. Numbers won't magically become numbers. (Actually, this isn't a feature of Zend_Config_Ini, but a misfeature of PHP's leaky typing.) You have to use # comments, rather than freely mixing #, ;, and //. And so on. Any of those features that you want to add, you'll have to add manually, just as you did this one.
As I suggested in a comment, if you really want to have more than two levels of hierarchy, you may be better off with a naturally infinitely-hierarchical format, where any value can be a list or dict of other values.
JSON is ubiquitous nowadays. It may not be quite as human-editable as INI, but I think more people are familiar with it than INI in 2014. And it has the huge advantage that it's a standardized format, and that both Python (2.6+) and PHP (5.2+) come with parsers and pretty-printers for in their standard libraries.
YAML is a more flexible and human-editable format. But you will need third-party modules in both languages (see the list at the YAML site). And it can also bring in some security concerns if you're not careful. (See safe_load and friends in the PyYAML docs; most other libraries have similar features.)