HII regions or emission nebulae are associated with the presence of massive stars that ionize the gas. The strongest emission line from an HII region comes from H-alpha. What happens in this case is that the hydrogen atom becomes ionized. Next, the electron and proton recombine to form a hydrogen atom again; however, the electron may be at any energy level. About half of the time, the subsequent downward cascade will be from transition n=3 to n=2. This emits H-alpha light which is in the deep red visible part of the spectrum. This line is one of the most common star formation tracers. I'm not sure if that completely answers your question, but most astronomers use H-alpha to detect HII regions, which is why I described its emission.
To add (in an attempt to clarify the various ways emission is detected), matter that is completely ionized is typically detected through free-free emission. In this case, there is no downward cascade of the electron to emit light the "typical" or most familiar way. Instead, emission is produced through free electrons scattering off of ions. Perhaps this is what you are referring to?
There is also synchrotron radiation, when charges particles accelerate in a magnetic field.
In any galaxy, a variety of emission types may contribute to a specific part of a galaxy, but there is typically one that dominates or is favored for detection purposes. For HII regions, H-alpha is studied because it is the strongest hydrogen emission line.
Oh, and H-alpha has a wavelength of 656.28 nm in air.
