'est-ce que`and 'qu'est-ce que' are really common in spoken every day language (between friends and family) but they are less used in writing and you will never find them in official statements or very polite situations. It really depends on the situation and the degree of politeness required.
Usually in polite / written texts, the question will be made by putting the verb first then the subject. Because that sounds quite formal, in spoken every day language we soften it by adding 'est-ce-que'.
'Est-il déjà arrivé ?' (polite) becomes 'Est-ce qu'il est déjà arrivé ?' (spoken, familiar language)
and if you need a 'what' (quoi) in your question:
'Que va-t-il faire ?' becomes 'Qu'est-ce qu'il va faire ?'
For me 'What's going on?' could become 'Qu'est-ce qu'il se passe ?' (pronounced 'kesskispass') if you're speaking to a friend but 'Que se passe-t-il ?' in a more formal situation (with every bit fully pronounced).
'What's wrong?' to a friend: 'Qu'est-ce qui va pas ?' (with people you know well you tend to skip the negative 'ne') or 'Qu'est-ce qu'il y a ?' (short for 'Qu'est-ce qu'il y a qui ne vas pas ?' I guess)
"non" can be used but like in English you usually just don't say 'No.' to someone's face, you soften it with a sentence to apologize or justify your position. Between friends and family it's more often pronounced 'nan' or 'nah'.
I think "n'est-ce pas", "c'est vrai", "vraiment" and "ah bon" are difficult to use because they tend to be used in a sarcastic or ironic way, but without full sentences it's hard to give other way of saying those.