There have been a lot of questions posed about exactly what parts/brands of the after-market will actually cause problems or void a manufacturer's warranty. Curious myself as to the actual bottom line, I ran across this write up on the SEMA website. It is fairly lengthy but definitely worth the read if you are planning to mod but are worried about this issue. Or if you have been denied a warranty claim it even walks you through how to handle the dealership and fix the problem. the link below goes to the full article, however i've extracted the key points and pasted below. hope this helps.
http://sema.org/main/semaorghome.aspx?ID=50096
The Law
Federal law sets forth requirements for warranties and contains a number of provisions to prevent vehicle manufacturers, dealers and others from unjustly denying warranty coverage. With regard to aftermarket parts, the spirit of the law is that warranty coverage cannot be denied simply because such parts are present on the vehicle, or have been used. The warranty coverage can be denied only if the aftermarket part caused the malfunction or damage for which warranty coverage is sought. Disputes in this area usually boil down to arguments over facts and technical opinions, rather than arguments over interpretations of the law.
The Magnuson-Moss Warranty Act (15 U.S.C. 2302(C))
This federal law regulates warranties for the protection of consumers. The essence of the law concerning aftermarket auto parts is that a vehicle manufacturer may not condition a written or implied warranty on the consumers using parts or services which are identified by brand, trade, or corporate name (such as the vehicle maker's brand) unless the parts or service are provided free of charge. The law means that the use of an aftermarket part alone is not cause for denying the warranty. However, the law's protection does not extend to aftermarket parts in situations where such parts actually caused the damage being claimed under the warranty. Further, consumers are advised to be aware of any specific terms or conditions stated in the warranty which may result in its being voided. The law states in relevant part:
No warrantor of a consumer product may condition his written or implied warranty of such product on the consumers using, in connection with such product, any article or service (other than article or service provided without charge under the terms of the warranty) which is identified by brand, trade or corporate name... (15 U.S.C. 2302(C)).