One such example is Open Runway, a company founded by Monika Desai, one of the strong members of the Boston mass customization community. Open Runway lets you crate individual shoes (soon) and handbags (now) and have them manufactured from scratch.
The web-interface is, as said, really convinient to use. You pick one of several base models, represented as silhouettes, decide which material and color individual parts such as heels, trims, straps etc should be in and see the results of your decisions in realtime on your screen.
As you can tell from the two images below, the process of designing is fairly simple even for men. Manufacturing time is announced to be 8 weeks, but if you have the chance to get the shoe or handbag, you have always wanted, what is two more months? (even if we know from our research that a delivery time of two weeks really improves the turnover rate .. so here is room for improvement for Monika).
More about Open Runway on their website. I am curious to see how this develops and fits into teh recent trend of strong investments into custom fashion sites.