The two theories are:
1. Particle-Wave Duality
2. Tunneling
1. Simply stated, the Wave-Particle Duality says that waves have some particle properties and particles have some wave properties.
A Jedi is made up of many particles, which can have some wave properties. Electromagnetic radiation is the most common example of a wave. Visible light is one form of electromagnetic radiation, but most electromagnetic radiation cannot be seen. (some other examples are microwaves, radio waves, x-rays, ultra-violet light, etc...)
If a Jedi spontaneously took on a waveform, his energy would still be present, but he would not be visible. The wave may later take on the particle form, and the Jedi would again be visible. However, while in waveform he may be detected by Force-users who can see other wavelengths besides the visible range.
We will have to accept that Jedi have a higher probability of taking of the waveform because they have more control over what their particles are doing. He leaves his clothes behind because he doesn’t have control over his clothes. However, because he is now in limbo between wave and particle form he can control how he looks to people by controlling his regeneration into particle form. Hence, Jedi usually choose to appear clothed to the living.
2. Tunneling is basically an particle going through a wall. Electrons do this a lot, because they’re very small, however, there is theoretically some probability that any object will go through any wall.
The Jedi can once again be in control of his particles as he dies and can tunnel through a wall of zero thickness into another dimension, where he is at one with the Force. To reappear, he simply tunnels back, and may reflect light at a different wavelength than the visible light range so he can only be seen by using the Force.
Because the probability of tunneling is inversely proportional to mass, a very tall person, such as Qui-Gon has less of a chance of tunneling than a very short person, such as Yoda. Most likely, the bigger the Jedi, the more skill it takes to disappear. But remember, no matter how big the Jedi is, there is always the possibility of tunneling.
While the true answer may lay somewhere between these two theories, or, more likely a few parsecs away, I think we are well on our way to discovering the secrets of disappearing at death.