Here goes. If I've done/am doing this wrong, please let me know.
The most important part of the phrase "public transportation" is the word "public." You are sharing a small space with strangers, and standard rules of etiquette apply, but here are a few special pointers when traveling on a city bus, commuter train or other short-distance public transport:
1. When you are waiting at a bus stop, and the approaching bus is not the one you want, please communicate your intentions to the driver before he or she stops. You can do this by stepping back from the stop, shaking your head "no," or waving him on courteously. If there are other passengers waiting, simply step back. If the approaching bus is yours, please step forward, attempt eye contact with the driver, and smile or raise your hand to communicate your intent.
2. When boarding a bus or train compartment in which the seats are full, step all the way to the back and find a good, safe handhold. Please do not stop in the middle or next to the door.
3. It is acceptable to place your bag, briefcase or backpack on the empty seat next to you only if the bus or train car is less than half full. It is preferable, however, to carry it on your lap regardless of the number of occupants. If you choose to set it down, be mindful of the point at which the car becomes half full, and pick it up before being asked.
4. When approaching a double seat that already has one occupant, ask politely if you may sit down, rather than expecting your potential seatmate to know your intention. This is especially important if the seat is occupied by the person's legs, feet or bag.
5. Exchanging conversation with your seatmate is not required, and may be considered an intrusion, especially if the person is reading, listening to music, or doing a craft such as knitting. However, a polite social exchange, if kept brief, is not out of place.
6. It is never incorrect to greet the driver when entering the bus, or thank him when exiting. In fact, some skills-development classes for the developmentally disabled teach them to always thank the bus driver when exiting.
7. Most buses, commuter trains, and the like have posted rules about not eating, drinking, smoking or listening to loud music. It's important to remember that, even if the rules are not posted or there are others around you violating these rules, it's still not polite to do so yourself.
8. If you're seated in front closest to the driver, don't engage him or her in unnecessary conversation, unless the driver encourages it. He or she has an important job to do and may not enjoy making conversation while negotiating traffic.
9. Keep your music, conversations, cell-phone exchanges, and other noises as quiet as possible, as a courtesy to your fellow passengers and to the driver.
