Houston has a few indy shops. I have experience with the following

Bavarian Machine
3117 D'Amico Street
Houston, Texas 77019
713-524-8365
Mike Perkins is the owner. He builds a lot of the club race cars around Texas and knows his stuff. He did the PPI on my M3 when I was selling it.

Matthews Auto
10400 West Montgomery
Houston, Texas 77088
(281) 447-0577
Full service shop, sales, and body shop. They are very involved with the Houston BMWCCA and sponsor a lot of the auto-x guys including me


Shop I would NOT recomend:
Bemer Preventive Maintenance
I took my e36 cabrio in there a few times after I first moved to Houston. They left off the AC belt one time, and lost the diagnostic port cover another, only to later find it melting on the manifold. The owner, Julian, seems to know his stuff but he spreads himself too thin and doesn't have the best help in there. I've heard others saying the same thing about this shop.