San Francisco Bay Area
Anything in the 9 counties, including the cities of San Francisco, Alameda, Oakland, Berkeley, and Richmond. Making this community wiki, so please add the ones you know. For those of you outside the bay area, it's 9 counties and about 40 different public transit agencies and there's all kinds of interlinks/transfer opportunities between them, so I think one big answer for all of the SF bay area might be the best way to present the information:
- BART (Bay Area Rapid Transit; light rail / subway connecting most, but not all of the bay area counties) — bikes are allowed on all trains, (during commute hours, not allowed in first 3 cars, or if the train is full). Folding cycles are always allowed. http://www.bart.gov/guide/bikes/bikeRules.aspx
- SF Muni (light rail, buses, cable cars, etc within the city of San Francisco) — Racks on the front of most buses, but not any of the other vehicle types. Folding bicycles are allowed inside all Muni vehicles (with the exception of cable cars) http://www.sfmta.com/cms/bcomm/BikesonMuni.htm
- Golden Gate Transit (GGT, crosses the Golden Gate bridge to connect San Francisco to the two counties north and also ferry service between Larkspur and SF) — racks on the front of some buses and racks underneath on others. Ferries allow a limited number of bikes. http://goldengatetransit.org/services/bikes.php
- AC Transit (Alameda country, with transbay buses to SF) — All busses have bike racks that hold two (or three on newer buses!) bikes on the front. Some also have storage space below that can hold (officially) 2 more bikes. Folded or collapsed bicycles may be carried on board anytime as long as they do not block seats or aisles. http://www.actransit.org/rider-info/rider-guides/bikes-on-buses/
- Caltrain (rail between SF and Santa Clara) — special cars for the bikes. Folding cycles allowed. http://www.caltrain.com/riderinfo/Bicycles/Bicycle_General_Info.html
- Samtrans (SF connection down peninsula to Palo Alto) — Buses are equipped with bike racks which hold two bikes. Two additional bikes are allowed inside the bus depending on passenger loads. http://www.samtrans.org/bikes.html
- Sonoma County Transit (primarily connects cities within Sonoma County and also provides local transit for some cities in the county) — racks on the front of every bus. Most racks accomodate 3 bikes, some only 2. If the rack is full and there's room on board, a couple bikes can go on board.
- Santa Rosa CityBus— Bike racks with 2 spots on the front. Can put bike in the wheelchair area if rack is full but bus isn't full.
- VTA Bus (Santa Clara Valley Transportation Authority Busses; Covers the South Bay Area) — racks on the front of every bus. Racks accomodates 2 bikes. If the rack is full 2 bikes are allowed inside, at the driver's discretion. http://www.vta.org/bike_information/bikes_on_transit.html