This is real easy to achieve.
You need to define a "module class suffix" in CSS, then set the module to use this suffix to apply the styling. The suffix normally would take the form of "-blue" or "-orange" but can be whatever you like. The suffix can be applied by entering it into "module class suffix" in the module manager.
In CSS, the suffixes are defined like this:
.moduletable-blue
.moduletable-orange
...and might looke something like this:
.moduletable-blue {
background: #44F;
color: #FFF;
padding: 5px;
}
.moduletable-orange {
background: #F44;
color: #FFF;
padding: 5px;
}
Any other .moduletable style definitions will not be inherited since you are creating new classes. You will also need to define new heading classes based on the new class:
.moduletable-orange h3
.moduletable-blue h3
And can assign specificity to them (say you only wanted these styles to apply to your left column, called "#leftcol":
#leftcol .moduletable-blue
...etc.
Hopefully that will get you started 
Dan