First I want to say that I have a legal kitchen and hate to ask this question so please dont beat me up. I have only made those small individual, one serving, square or round wedding cakes that require their own small cake board and are generally accompanied by an anniversary tier  presented on a cupcake tower one other time and might I add, I hated them. They were definately more work than I had anticipated for what I charged. My question is what SHOULD I be charging for these annoying little cakes? They will be covered in fondant of course. Thank you in advance.

AAdd up your ingredients, labor cost, and overhead then add your normal markup.

If you charge properly by the hour (like 3X minimum wage) plus for other stuff as Jason says, then you should indeed have small cakes that cost a LOT.  Unlikely that you will sell many (smile).

Maybe you should only offer the petit fours type:  production line of sheet cake, filled single layer, buttercream top, cut into squares or circles, covered with poured fondant. These can be any size you like.

Decorating with fancy piping is not hard when you use small tips,  and these take a whole lot less time  than the utterly thankless work of rolled fondant.  They will be smooth and taste a heck of a lot better...and you will feel better while making them.

I charge at least $50 each for those stupid little things...But you can sell them (assuming you want to do them) to the bride by pointing out that she can avoid larger floral centerpieces if she uses the cakes, so she'll have money in the budge that would otherwise go to flowers.