This article tries to put on record exactly why OPERA neutrino anomaly, FLYBY of Galileo anomaly and PIONEER anomalies are not at-all anomalies, based upon my research from late 2011. On 25.11.2013 I sat for couple hours and reviewed the article written from 2011 and added contents. Since I am reading after couple of years I reminded myself exactly why these are not anomalies: and here is why. 

Anomaly from OPERA experiment involving neutrino base line:
The mass of elementary particles is equivalent to a proper-time and in another way to the Compton-wavelength. Compton wavelength is defined as $latex \lambda_{Compton} = \frac{h}{mc}&bg=ffcccc&fg=cc00ff&s=1$ where c is the speed-of-light in appropriate units, m is the mass of a given particle, note that h is the Planck’s constant, not the reduced Planck’s constant, usually found in quantum mechanical treatments.

So in case of the OPERA experiment, the neutrino howsoever it challenged the physical validity of the sanctity of proper-time of photon — that proper time of photon is always zero and minimum among all elementary particles, because its a tiny little smurf with hardly any-mass, it could not run faster, because it has mass.

Again the energy uncertainties of the experimental detector would equivalently add mass to the neutrino, a fact completely over-looked by OPERA experiment collaboration.

Photon proper-time is defined to be least, because its mass is zero, hence neutrino must always take more time than photon, for traversing the same distance, but OPERA claimed otherwise. All in all Relativity + Quantum Mechanics restores the anomaly to its nemesis. 

Anomaly from FLYBY of Galileo and PIONEER satellites:
For an explanation of the anomalies while equivalence or relativity of mass, momentum, energy, wavelength etc are not needed here, whats simply needed is mass. This mass is a Newtonian concept but rather refined by Einstein’s theory known as Theory of Relativity which branches into two aspects 1. special theory and 2. general theory.