I've added additional options applicable to filled line plots, fillAndStroke, fillAlpha and fillColor. A patched jquery.jqplot.r239.js and a sample test1.html files are attached to the ticket.
fillAndStroke: If true, will stroke a line on top of the filled area (default is to just fill the area up to the line.
fillColor: If fillAndStroke is true you can specify a custom fill color with fillColor. The default is the line color. You can specify alpha transparency directly in the fillColor spec as so: fillColor:'rgba(126, 239, 44, 0.5)'.
fillAlpha: If fillAndStroke is true, this will add alpha transparency to the fillColor spec of the line. If transparency is already specified in the fillColor spec, it will replace that transparency. fillAlpha is useful if you want the default fillColor to be used, but just want to make it transparent.