how do i make my matron of honor stand out form the rest?

you could get something for her to put in her hair. You could give her different colored flowers, maybe put something sparkly in or on the bouquet, maybe add some extra ribbons to her bouquet.

Do the dresses have belts? If so, you could make hers different from the rest. As for the flowers, make their ribbons one color and hers a different shade. Is there something you can do to the bodice of her dress? Make it lower cut, higher cut, etc. How about her hair? Have the other girls wear their hair one way, and hers different. Other than that, I can't think of anything. Sorry, but good luck.

I always thought i would put my maid of honor in a different dress, that still goes with the same colour theme but easily stands out, As my matron of honor is probably the second most important person in my life.. but more subtle ways...some headpiece or accessory...something a little more luxury?

The usual way is to put the MOH in a different SHADE of the same color as the rest of the girls or change her bouquet enough to be a bit different.

For my wedding I had dark blue dresses and white shawls for all the girls, but my MOH wore a silver and white brocade shawl to set her apart a bit.

fancier shoes? Headband, pin or comb? brooch or some other form of jewelry? gloves? sash, wrap, bolero or jacket? if the dress is strapless, you could add a sleeve to hers, maybe... (David's Bridal does it on select styles)

A white sash, maybe? Try not to make it too unsightly.