Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
What is the ruling on wiping over socks?
It is not permissible to wipe over most common socks today because the conditions for wiping are not met. The concession was reported for wiping over leather socks (khuff) and socks (jowrab) with conditions: They must be thick, not allowing poured water to penetrate, enable one to walk in them, be worn while in a state of purity (from ablution), cover the entire foot up to the ankles (meaning covering the protruding ankle bones), and not be torn. And Allah the Almighty knows best.
What is the ruling on water present on the floor of a toilet/bathroom?
The default ruling is the purity of this water present on the bathroom floor. If one is certain or strongly suspects its impurity, then one washes whatever part of the body or clothing this impure water has touched. If one doubts its impurity, the default is purity, and we do not rule it impure based on mere doubt. And Allah the Almighty knows best.
What is the ruling on entering the toilet with something containing the remembrance of Allah?
It is disliked to bring into the toilet anything containing a reminder of Allah, such as the Quran or a sacred name (like the name of Allah, Muhammad, etc.). If one does that, etiquette dictates that he conceal it so it is not visible while entering the toilet, either by cupping his hands over it, putting it in his pocket, or inside his shirt if it is a necklace or ring. And Allah the Almighty knows best.