Personally, I'll base a lot of quirks and flaws off significant backstory moments and what the character does most of the time.

Example: Bard/shadow attack survivor who was scared of being alone in the dark and would press into whoever was holding the torch during underground missions. He was also the primary face and was suave, smooth, and charming in public... but was frankly worn-out by all the social manipulation and let his guard down when he was alone with the party. More snark and world-weary comments.

Being an ex-spy, he would also sometimes take a shady route to help. Like drugging the wizard's food and drink after too many downtime all-nighters in the name of research. (Wizard's player had fun making this a running gag with me.)



Other times, it's just a fun thing that pops to mind while playing or a bit of wordplay.

Example: Investigator character who was very "grounded" in personality and the mental image I had when building her. Further in, when the group first had to travel by helicopter, I thought it would be amusing if she preferred being literally grounded as well and had it come out she hated flying. Still a tough-as-nails character, but one who had to spend the trip with eyes squeezed shut and fingers burrowed into the seat cushion.

Character was also a coffee fiend prone to all-nighters and probably could have used a teammate proficient in subtle sleep drugging.