Some of the current "mass customization" players as noted on the mass customization blog. It is an interesting list and often involves tweaks in the final product that don't dramatically affect the design. There is also a skewing towards premium priced products,.
There is enormous potential here, but building cost effective production systems and workable business models is still a major challenge. A few companies that are doing mass customization and/or co-creation are Zazzle, Theadless and a few other custom tshirt houses. Apparel is a juicy target as so many people don't get what they want.
I have an interest in the fit of objects, which is a more complex problem than changing some ingredient sin an energy bar or specifying the colors and materials in a hand bag. There is still a long way to go for clever people.
For now if you really want something custom the best route is to make it yourself (if you can) or find a craftsperson.