When it comes to materials like windows, doors, hardwood flooring etc, what are your go-to brands?
You are asking a question so open-ended that it's virtually unanswerable with any valuable information. "Go-to" depends on a specific design, budget, regional availability, etc.
You really need to work with your architect and builder to explore and work these things out, after you have your design completed. It makes no sense to start with such an effort before your design is completed.
A good way to get a handle on this however, is to tour new homes and take notes. Even if you do this, however, you will never accumulate the quantatative and qualitative information in the minds of experienced architects and builders, not to mention available on their technical information bookselves. That's why you should use them.
Good luck on your project.