A lot of them are done using 'simple harmonic motion' applied to the r,g,b channels.
SHM looks like this:
value = amplitude * sin(frequency * angle)
In our case, for a plasma, we want rgb values to come out, any one of these channels has a range 0-255. We know that sin(anything) goes between -1 and +1, so to scale that we need to do
value = 127 + 127 * sin(frequency * angle)
That will give us a number between 0 and 254, which is good enough.
Now we need to look at the frequency * angle bit. Usually you want this number to be some function of x, y pixels (x+y will do for a start), and you want the frequencies of the r,g,b channels to be different, so you might have something like:
red = 127 + 127 * sin(1 * (x+y))
green = 127 + 127 * sin(3 * (x+y))
blue = 127 + 127 * sin(5 * (x+y))
colour = (r<<16)+(g<<8)+b
That will give you a pretty rubbish plasma, but it gives you the idea. Almost all the cool Amiga plasmas were done by combining different functions for (x+y), and combining other trig functions such as cos, tan and the rest.
Other great plasmas can be done using 'Perlin noise' which is worth plugging in to Google.
Jim