Yes Cobb in my opinion is the best turner all around for a couple of reasons. There are literally thousands of tunes you can download for it and a large following. I have JB plus at the moment but as soon as I install my new FMIC I will remove JB plus and go with a Cobb AP Stage 1 tune. Many good tunes out there but the shear volume of Cobb tunes makes it heads above the rest.
If you want the PhD information on tuning the N54/55 engines go to bimmerboost.com. Our forum is excellent but general in nature. Bimmerboost is totally about those engines and a few others.
Expect to be overwhelmed with information...