Semiconductor quantum dots (QDs) are fascinating nanoscopic structures for photonics and future quantum information technology. However, the random position of self-organized QDs inhibits a deterministic coupling in devices relying on cavity quantum electrodynamics (cQED) effects which complicates, e.g., the large scale fabrication of quantum light sources. As a result, large efforts focus on the growth and the device integration of site-controlled QDs. We present the growth of low density arrays of site-controlled In(Ga)As QDs where shallow etched nanoholes act as nucleation sites. The nanoholes are located relative to cross markers which allows for a precise spatial alignment of the site-controlled QDs (SCQDs) and the photonic modes of high quality microcavites with an accuracy better than 50 nm. We also address the optical quality of the SCQDs in terms of the single SCQD emission mode linewidth, the oscillator strength and the quantum efficiency. A stacked growth of strain coupled SCQDs forming on wet chemically etched nanoholes provide the smallest linewidth with an average value of 210 µeV. Using time resolved photoluminescence studies on samples with a varying thickness of the capping layer we determine a quantum efficiency of the SCQD close to 50 % and an oscillator strength of about 10. Finally, single photon emission with associated with g (2) (0) = 0.12 of a weakly coupled SCQD -micropillar system will be presented.