Cervelo if you are a serious rider. Cervelo also makes THE BEST velodrome bike in my opinion. So if you are planning on becoming a track cyclist then look no further than Cervelo. Cervelo IS THE BEST in my book for all road bikes. However if you want a company outside of North America then look into LOOK bicycles. Its a french boutique company that makes EXCEPTIONAL frames and also other bike components.
If you are looking for a good bike company that will sell you a COMPLETE BIKE then go with TREK if you have a minimum of $3,000 to invest in a decent road bike. If you are not buying a road bike then look elsewhere.
The best Mountain bike company in my opinion is Specialized. They also happen to make nice road bikes. Also specialized invested heavily in research and they got some technology that other bike companies dont have, such as the Zertz inserts which significantly improve road feel by absorbing vibrations that cant be absorbed by just carbon fiber frame. Tom Boonen won the Paris-Roubaix in a Specialized Roubaix S-Works bike that has zertz inserts. Its one of the most comfortable high-end road bikes out there. But you need atleast $8,000 to purchase this bike.
If you are looking for a bike under $1,000 then go with Kona. This is one of the best companies for entry level bicycles as they usually put components that belong on bicycles much more expensive on their less expensive bicycles.