What is the "lowest energy"? In many textbooks I come across the term lowest energy. For example in atomic structures, electrons are placed in orbitals in order for the atom to have the lowest energy. But what is this energy? Potential- or kinetic energy or the sum of the two?
 A: The lowest energy of a quantum system is the minimum eigenvalue of the Hamiltonian of the system. The Hamiltonian is the operator which corresponds to the total energy of the system, so it is the sum of the kinetic and potential energy. This is often also referred to as the ground state energy of the system.

but what is this energy? 

Heuristically, the ground state energy is the energy which the system has simply by existing. Normally, this doesn't make any sense: If I just make the system do nothing, just sit there, then it would have zero energy. We wouldn't need the fancy name.
But it turns out that this is impossible. We can never "pin down" a system and make it completely still, due to the famous Heisenberg uncertainty principle, 
$$\Delta x \Delta p \geq \hbar/2.$$
The system must have some momentum, to satisfy the inequality. In turn, it will also have some energy. This is why we can never reach absolute zero! No matter how hard we try, there always remains the jiggling of the ground state.
A: The sum of the two.
An electronic state like an orbital is an exact or approximate solution of some time independent  Schrödinger equation, i.e. an eigenstate of the hamiltonian made by a kinetic and a potential energy term. The corresponding eigenvalue is the expectation value of such hamiltonian, evaluated on the state described by the orbital. 
The expectation value of the hamiltonian  can always be written as the sum of the expectation value of kinetic and potential energy. The lowest energy, is the eigenvalue of the hamiltonian with the minimum value. 
A: In QM the Schrödinger Equation gives you the solutions for the wavefunction of a particle with a given potential. Because the energy is quantized you usually find several possible values for the energy that are given by an integer number $ n $ called the Principal Quantum Number. The lowest value of $ E_n $, normally when $ n=0 $ or $ n=1 $, is the Groud-State. This means that the energy of the particle is the lowest and it is a combination of the potential energy and the kinetic energy.
