It's a matrix of sorts for me and includes the following factors, most certainly not necessarily in order of importance:

1. frequent flyer program benefits and ease of use
2. schedule/schedule convenience/flight time
3. in-flight communication/work facilities
4. type of aircraft
5. in-flight product/amenities (seat, entertainment, etc.)
6. ground facilities (particularly shower suites and lounges)
7. in-flight service (food, cleaniless of bathroom and its supplies)
8. ground service
9. safety record
10. ease of booking tickets (i.e., etickets, close to departure ticketing possibilities)
11. cost of tickets
12. personal contacts with airline/airport employees available to facilitate special needs