Vt = 25 mV is a thermal voltage at room temperature, about 20 degrees Celsius I believe. This value changes with temperature.
It comes from semiconductor physics where you try to describe a PN junctions diode, you arrive at Shockley's equation which describes its IV characteristics. It turns that the Shockley's equation is highly non-linear.
BJT transistors are composed of two such diodes which also behave non-linearly. So ultimately, when you try to describe the behavior of BJT transistor amplifier, it will be non-linear. But because it's difficult to deal with non-linear equations, the diode equations have been linearized by making some assumptions into what is called the small-signal model. As a results a couple of new parameters come into play, such as r_e, r_pi, g_m.
When you work this out, Vt makes its way into the linearized model and that's why see it.
For more info check out: Sedra/Smith.