The Bus system in Puerto Vallarta might best be described as "Eclectic". Buses of all shapes, sizes and decoration cover all of PV and are very inexpensive. That said, it is very efficient if not luxurious. The main routes for tourists are from the Marina hotels and Condos to downtown and vice versa. If you are traveling from town back to the Marina, make sure that somewhere in the many words and pictures decorating the front window you'll see "Marina" at the top destination window of the bus, some busses will have Marina on the windscreen, but do not go into the Marina hotel area. Bus stops are generally well marked and the buses usually operate on about a 15 minute interval. Late night it is better to take a taxi as the routes become more diffuse and less reliable. 

Buses in Puerto Vallarta are very high off the ground; hence, getting on and off can be difficult for the elderly or someone with bad knees, weak legs or other mobility difficulties.  Also, unlike in most buses in the US and Canada, you have to push a button (called a "timbre") for the driver to stop.  These are located, usually near the front, near the back exit, and several other places throughout the bus.   The doors on the buses have no automatic release mechanism so if  a person is slightly slow getting off, they might find the driver closes the door on them before they have exited the bus. 

Locals with disability cards are allowed to get on the bus and ask for donations from passengers, also entertainers will sing and/or play a musical instrument for tips.  

The 1st two seats behind the driver are reserved for people with disabilities and pregnant women.

Taxis are not metered but there are government set fares by zone.  Fares to various places are posted outside most hotels and resorts so travellers should do their homework and insist on the set fare.    The typical fare from town to the Marina is around $4-$5, or 40 - 50 pesos depending where you start from.  It is more expensive by about $10 pesos to go south of the river (South side, or Zona Romantica), i.e., $6 or 60 pesos.   It is not necessary to tip unless you feel the driver was particularly informative or helpful.

If you are staying in the Hotel Zone, look for buses that contain the listing Hoteles on them.

If you want an interesting side trip with the buses, take the TUNEL bus.  It will take you around the city through a tunnel in the mountain, then back in to the city on the south side (Zona Romantica).  It does not cost any more pesos.  The locals use it more than tourists and it gives you an interesting perspective of life away from the tourist area without having to leave the bus.