Dinan is the only aftermarket supplier in the US that works with BMWs warranty. As I understand it, Dinan takes over the BMW warranty on the car in any fields where a Dinan component could cause damage, and on the Dinan parts themselves. For more information check out this link.
http://dinancars.com/Warranty.asp
I have Dinan parts installed on my car and I think that they are the way to go with newer BMWs. Dinan tends to put alot of research and development into their products so that the cars don't get that "modified feel" you get with many tuners. Dinan cars feel just like an origional BMW product, just with better handling and more power. Thier products also tend to be alot more reliable then the competition.
Dinan Pros- warranty, reliability, feel
Dinan Cons- initial cost, power gains
Another option that alot of people are turning to is a company called Active Autowerke. They offer a supercharger kit for the E46 that will get much better gains then Dinan for less. Where as Dinan will have you around 250hp (maybe), the AA S/C kit should have you around 330-340hp, which is M3 territory. The Dinan S2 330Ci ZHP kit costs around $8,000, while the AA kit costs around $6,500. The Dinan kit comes with suspension upgrades which AA doesn't, but the AA supercharger's power blows Dinan away. The downside is that many people think that AA rather unreliable.
Good luck with the car.