Unfortunately, it's not something that is in the generic settings for appearance, you have to change it in gconf-editor or the command line. I'm going to make it semi-transparent in the next release so that it won't clash with anything, but in the mean time you can open a terminal (ctrl-alt-t) and type gconf-editor, then navigate to /apps/panel/toplevels/top_panel_screen0/background/color and change it there. To select a color, use the GIMP to either pick a color using the color selection tool or use the eyedropper tool on a portion of your background image to select a color, then copy and paste the value in HTML notation to the /apps/panel/toplevels/top_panel_screen0/background/color field. Be sure to precede your color with a "#".
If you're feeling adventurous, you can do this even faster from the command line with:
gconftool --type=string --set /apps/panel/toplevels/top_panel_screen0/background/color "#0055a3"
(replace "#0055a3" with the color of your choosing)