Some considerations when choosing are:
What are you getting? While many B&Bs are luxurious, they range all the way to sub-bargain. Find out what you can expect. What bed sizes are available? Are the pillows foam or down? Is the bathroom shared? What is the breakfast selection like and is it included in the price?
Location, location, location. Research the area first. Is the location convenient to the attractions of the area? If you will be using public transportation, is it nearby? Is the neighbourhood safe and aesthetically pleasing?
Pets. Do the hosts have pets? Dogs and cats are not uncommon. Are guest pets welcome?
Children. If you are bringing any, make sure they are welcome. If you don't want any around, make sure they are not.
Non-smoking (or smoking) rooms? Is it a smoke free environment?
Ask if your special dietary needs can be accommodated.
Are advance reservations required? What is the cancellation policy?
What are the check-in/check-out times? Typically B&Bs have a stricter policy than a hotel. There won't be a 24-hour desk clerk to check you in at 02:00 if you are running badly late; breakfast is also usually only available at set times or by agreement.
Is there a minimum stay?