There are a few different types of garage door companies out there. There are huge national companies, large local companies operating dozens of service and installation trucks each day, smaller local companies operating just a few, and individual owner/operators.
When it comes down to it, what really matters is the experience and attitude of the guy who comes out to fix your garage.

Big National Garage Door Companies
There are a handful of major, nationwide garage door companies.
In my experience, these companies tend to use hardcore upselling tactics and have employees who are trained to be sales people above all else. You are likely to encounter an inexperienced technician who was hired for his sales ability. His goal is to sell you a bunch of unnecessary stuff, and his pay may be 100% commission based.
There are other national companies that specialize in commercial work and aren’t especially interested in dealing with residential repairs.
Unless you live in a location without many options, I wouldn’t use this type of door company. You are likely to find better service and pricing from a local company.

Big Local Companies
Many large metropolitan areas have one or two large local garage door companies. These could actually be the biggest companies in your area with dozens of trucks on the road every day.
This is worth investigating, you may find a really great company with hard to beat pricing and service, and experienced technicians. This was at some point a smaller company that really did things right.

Medium Sized Local Companies
Most cities have multiple, or even dozens, of local “mom and pop” type garage door companies that employ 10 or fewer technicians/installers and have a few trucks on the road every day. You could find a really good company in this mix, but there are some unbelievably bad ones, too. It is important to check reviews and ask questions on the phone while booking your call, and trust your gut. If they are reluctant to explain pricing or warranties, move on.

One man owner/operator
This is another one that could be great, or could be incompetent or unreliable. Make sure that you have found someone who seems to advertise professionally, has a website, drives an appropriate vehicle (not a minivan), etc. There are a lot of expert garage door guys who do very well as a solo operation. The most likely problem here is reliability, so make sure you trust that the guy you talk to on the phone will actually show up, and be sure that they are appropriately licensed.
One big advantage here is that you are likely to be talking to the owner of the company on the phone. If he is an honest guy, he can do a better job working with you and answering detailed questions. With bigger companies you are probably going to be talking to an office person who doesn’t really know that much about the specifics.
There is also far less chance for miscommunication, assuming you are talking to a guy who is reliable. Like in many service businesses, office miscommunication causes the majority of misunderstandings and bad experiences.

Note: Whenever you choose one of the medium to large door companies, you are going to be talking to a receptionist/call booker on the phone. This person probably doesn’t know much about garage doors. You should be able to get basic pricing for common, standard services, but do not expect accurate answers to detailed questions. This person may also be paid in part by how many calls they book, which can lead to over-promising. Or it could be a call center in another state. If you will be extremely frustrated if the technician and office don’t seem to be on the same page, try to find a competent owner/operator type company.
Also, don’t be surprised if it goes to voicemail when you call an owner/operator. But if it isn’t a professional, friendly sounding message, hang up and try someone else, there are good guys out there.