Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?
It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.
What is the ruling on performing ablution (wudu') and ritual bathing (ghusl) with Zamzam water?
It is permissible to perform ablution and ritual bathing with Zamzam water. However, scholars disliked using it for cleaning after relieving oneself (istinja'). And Allah the Almighty knows best.
What is the ruling on vomiting, and does it invalidate ablution?
Vomit is impure (najis). Its exit is not considered one of the nullifiers of ablution. However, the mouth must be washed and purified from it, and any that gets on clothing or the body must be washed for prayer, because prayer is not valid with impurity present on the body or clothing. And Allah the Almighty knows best.