Wily Cycles has mainly specialized in making customized frames and only do the 29er thing.

They are offering something a little different now though. You can get their Classic Mountain 29er frame in four stock geometry sizes, however:

1. the frames are still unpainted, so the customer gets to pick the paint color and full custom paint schemes are possible
2. they are available in a regular geared version and single speed. The optional braze-ons and a derailleur tab right dropout allows the ability to run gears. The sliding dropout option allows running single speed

So this allows you to pick up their frames for a lot less money then fully custom built.