Home Decorators Collection has added custom upholstered beds to their options. They offer a variety of forms from nail heads to no nail heads, wing back, etc. Their fabric options are somewhat limited, but you may find something you love. They do offer coordinating pieces to go with the beds. This Kenter Custom Arch Bed is one example of what they offer.
Ballard Designs offers more options for you on upholstered beds. In addition to the more than 125 fabrics that they offer to their customers, they also offer the COM or Customers Own Material option for a truly custom look. For their standard fabrics they have a very user friendly website that allows you to easily search by fabric category and color and then view your bed in that fabric selection. This way you are more likely to know what you are getting with the scale of the fabric on this item. This Louisa Bed is shown in the Ikat Medallion
I love what can be done with truly custom upholstered beds done through workrooms. This bed by designer Jennifer Flanders is stunning. I just love the detailing that she created with nail head trim.
Here is a pair of custom upholstered twin beds by ARDEN Interior Architecture & Design done for the 2010 Hampton's Designer Showhouse.