Consider yourself blessed. NY airports are a nightmare. Same with LAX, ORD, ATL, DEN, and most other major hubs. (DFW seems to be a sole exception to the hubs-are-sucky axiom; I've rarely has anything but pleasant experiences from that airport, and I think I've connected through it over 100 times in the last 12 months).
Of all of these hubs, I hold a special pocket of hatred in my heart for my hometown airport, LAX. It's not the biggest or most crowded airport in the country, but it seems to be the worst run. Security lines take at least 45 minutes a pop, even if there are only about 10 people in line. Pre-takeoff delays on the tarmac routinely run 60 minutes or longer. Etc. It's about as well-managed as a DMV, and every bit as infuriating.
SFO tends to suck, too. I'm actually surprised you haven't had worse experiences there. It's routinely rated as one of the worst airports in the country for delays. (SJC, by comparison, ranges from painless to downright pleasant).