Resonant entrainment of oscillating systems is a well-understood principle within the physical sciences. If a tuning fork designed to produce a frequency of 440 Hz is struck (causing it to oscillate) and then brought into the vicinity of another 440 Hz tuning fork, the second tuning fork will begin to oscillate. The first tuning fork is said to have entrained the second or caused it to resonate. The physics of entrainment apply to bio-systems as well. Of interest here are the electromagnetic brain waves. The electrochemical activity of the brain results in the production of electromagnetic wave forms which can be objectively measured with sensitive equipment. Brain waves change frequencies based on neural activity within the brain. Because neural activity is electrochemical, brain function can be modified through the introduction of specific chemicals (drugs), by altering the brain's electromagnetic environment through induction, or through resonant entrainment techniques.
The effects are strongest while you are listening to the tones because your brainwaves are synchronized and tuned into the frequency range you desire at that time. After you've stopped listening the effects can still linger for a while afterwards. The timescale will vary from person to person and be affected by what you do after you've stopped listening.
You are already far beyond the need for using an entrainment product as a meditation aid. Those who sincerely believe this to be the case would not have come searching for a meditation site such as Project Meditation to help them learn and practice meditation and brainwave entrainment. They would probably not even bother with using an entrainment aid; hence this entire discussion would be irrelevant to them. The fact that you are here, reading this, seeking to benefit from incorporating meditation and brainwave entrainment to aid in your existing meditation practice suggests you are not one of these folks whose development is so advanced that entrainment is of no use to you.
Most of these websites give some brief explanation of entrainment. The example you hear most often is that of Dutch polymath Christiaan Huygens, who in 1665, hung two pendulum clocks next to each other on a wall. He noticed that the pendulums eventually matched each others' frequency, but always in antiphase, opposite to each other, as if canceling each other out. He'd try disturbing one or setting them in sync, but they'd always return to the same antiphase synchronization. Huygen's experience is widely touted on binaural beat websites as a demonstration of how systems can become spiritually connected through some energy field. However, they misunderstand what happened, and have not read the full story. Huygens also tried taking one clock off the wall, and as soon as they were no longer physically connected to one another via the actual wall, the effect disappeared. It was not the proximity of the clocks to one another that created the entrainment; it was their physical, mechanical connection to one another. As each pendulum swung it imparted an infinitesimal equal and opposite reaction to the wall itself. With two clocks on the wall, the system naturally sought the lowest energy level, according to the laws of thermodynamics; and both pendulums would thus swing exactly counter to each other, minimizing the system's total energy.
From a strictly physical/emotional viewpoint, the benefits of meditation include (but are not limited to) such things as greater resistance to stress; less physical illness and improved resilience when illness does occur; better quality of sleep and increased recovery during sleep; a generally magnified sense of well-being; a sharper, clearer mind; increased capacity for learning; improved functioning in daily life; more harmonious relationships; greater control over emotional states, and more.
For example, according to Wikipedia, if you take one frequency in one speaker in a pair of headphones, say, 300Hz, and the other speaker for your other ear has a frequency of 310Hz, the resulting difference of 10Hz would be the rate that the pulse, or beat, plays at. 10Hz (Alpha Waves) would correspond to what the brain puts out when you are generally relaxed. So, in effect, listening to a 10Hz binaural beat for a certain amount of time should take the edge off.
The activity of neurons generate electric currents; and the synchronous action of neural ensembles in the cerebral cortex, comprising large numbers of neurons, produce macroscopic oscillations. These phenomena can be monitored and graphically documented by an electroencephalogram (EEG). The electroencephalographic representations of those oscillations are typically denoted by the term 'brainwaves' in common parlance.