In the USA alone, there are thousands of mountain bike brands.  The four largest are Trek/Gary Fisher, Specialized, Giant and Cannondale.  The "big four" offer the largest selection of entry-level to race-level bikes in cross-country, trail, all-mountain, freeride and downhill; geared and single-speed; 26" and 29" wheels.  That, combined with a great warranty, makes the "big four" bikes a great value.

American bikes with a little more "wow factor" and a high-end niche market are Ellsworth, Turner, Titus, Niner, Yeti and Ibis, to name just a few.  Each of these smaller brands have a faithful following and some have achieved near-cult status among their riders.  Local frame builders such as Dean and Moots have a large, mostly local fan base, although they are available worldwide.  Most of these higher-end companies don't have any entry-level bikes at all.  They are geared toward serious, advanced riders who don't mind spending more for a boutique name and status.  Boutique brands don't necessarily build their frames in-house.  Many are built overseas, so if buying a locally made frame is important, be sure to ask!

Riding a custom mountain bike is less common than riding a custom road bike.  This may be because it's difficult to spend a lot of money on a beautiful custom frame and then have a spectacular wreck - they are not inexpensive to replace.  However, there are a few companies that offer both custom and stock mountain bikes:  Moots and Independent Fabrications are great examples of US frame builders.

Beware of buying a bike just like the racers' bikes - they are lightweight and fast, but also super-expensive and potentially more fragile than "everyday" bikes.  Be sure to look for a bike right for your intended use, and your budget.