Tips from a daily commuter for 2 years:
Avoid BART at peak commute hours (towards SF in the morning, and away at night) if you can... You can never get a seat and people are grumpy.
There is an unspoken rule about lines for each "door" marked in black on the floor. Most people won't say anything, but it is super annoying when people jump in, especially if they were waiting at the 10 car spot for an 8 car train then they try to jump in front of you.
Don't try to catch the doors as they are closing... If it closes on you it wont hurt, but the doors get jammed and everyone has to get off until they send a new train...
Always check the news to see if the BART drivers are threatening to strike... They have benefits most working people wouldn't dream of, but still hold the bay area hostage once in a while because they deserve better... I'll only support that when I get parking and a seat everyday and every train is on time.
Guys - Don't take the seat reserved for elderly and handicapped... Do you really want to have to "guess" if she's really pregnant, or just large? If you see someone visibly pregnant and are willing to risk it, tell the punk kids to get up for the lady...
I think that's all I got for now, but I could probably go on forever.