Just to make sure I totally misunderstand, render this:

#version 3.1;
global_settings {assumed_gamma 1.0}
light_source {
   < 500, 500,-500>
   rgb 1
}
camera {
   location  <4, 0, -10>
   look_at   <4, 0.0,0.0>
   angle 90
}

#declare yy_off=sin(clock*10*pi/5);

#declare xx=0; #while (xx<=10)
  #declare yy=sin((xx+clock*10)*pi/5)-yy_off; 
  #sphere{<xx,yy,0>,.5 pigment{rgb<1,0,0>}}
#declare xx=xx+1;#end

with clock going from 0 to 1 (the number of frames is up to you, I tried
20). Apart from the fact that the distance between the spheres isn't
constant (which is easy to fix) what's wrong with it? I guess this is
not what you're looking for but I don't see what is.
And as for Greg's remark ("The sin cos solution prevents non unique
positions along the x axis.") this shows that there's no problem there.
I didn't say you had to use sin AND cos, just one of them is enough, or
use a clever combination to get more interesting wave-forms (I have a
little program that can illustrate that).

Bye,

Remco

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