Considering the speed of light, any number of photons carrying the same colour frequency and hitting the retina at the back of an eyeball would be at varying phases in their respective cycles, but they can all impart their colour frequency. This baffles me. Am I right in saying that a photon emitted from an electron is "pulsing" at an energy level and frequency which determines it's colour? What drives the oscillation anyway? I can't help thinking that we are talking about ideas and not hard science. Is there any proof to these photon theories?
Am I right in saying that a photon emitted from an electron is "pulsing" at an energy level and frequency which determines it's colour?
No, you are not right; photons do not pulse in real time and space.
Photons are quantum mechanical entities, elementary particles in the standard model of particle physics. (Their complex wavefunction has oscillations but that is another story). They just have energy= $hν$ where $ν$ is the frequency the classical electromagnetic light has, which is built up by the superposition of zillions of photons, and h the Planck constant.
The cones of the retina, are composed of atoms and molecules,and the atoms and molecules absorb the photon in an energy level which will signal to the biological set up of the retina that light is coming in.
It gets even more complicated, because the biological computation path generates color perception: i.e. an electromagnetic frequency corresponds to the color of the spectrum according to frequency, but the perception of color is wider, frequencies add up to the same color perception:
To add to Anna V's answer: the mechanism by which photons are detected in the eye is indeed based on their energy, which is $h\nu$, where $\nu$ is frequency.
What happens is that there are proteins in the eye called Photopsins, which use retinal (which is a form of Vitamin A). When this absorbs a photon of the correct energy, it changes configuration, and it's this change in configuration that the eye ultimately detects.
And the important thing is that the system depends on the energy of the incoming photon: if the energy is in the right range, and so the frequency is in the right range, then the configuration change happens, while if it's not, it doesn't.
Needless to say, like almost anything that has had billions of years to evolve, the actual mechanism of detection is intricate, to put it mildly.
Concerning your question 'is there any proof to these photon theories?': there is very good evidence for them indeed, because we can detect individual photons (indeed some animals, possibly including humans, have eyes which can detect invididual photons). See this question and this answer (also by Anna V).