A bus stop look like this, but some have disappeared or are hidden pretty good. Just look for a crowd of people on the street, since the busses run very frequently, it will be easy for you to spot the stop.

Getting to Town by Local City Bus

6.5 Pesos to almost everywhere, unless you go out of Puerto Vallarta.
Example: The South Side of Vallarta to Boca de Tomatlan (about 6 miles south) is 7 Pesos. To El Tuito is 20 pesos.
No longer do you share your ride with live chickens, at least I haven't seen any lately. But you may have live entertainment, all for 6.5 Pesos! Note: they are trying to increase the fare to 7.5 pesos - on hold right now.
If you are traveling light, the bus stop at the Airport is right outside by the pedestrian bridge, you'll see some Resort Busses there, but look for a group of locals - they will be waiting for the bus - the middle exit goes to airport taxis and the parking lot. The yellow cabs are across the road, which is going north and they have to drive to the Central Bus Station road to turn around, which they say is another fare zone, so you only save about 20 pesos.
To get to town from the Hotel Strip and the Marina take the bus that says 'Centro' and does not have 'Tunel' on it, this one will take you through Downtown and on to the south side terminal. The ones which have 'Tunel' bypass downtown, but still end up at the terminal on the South Side by Parque Lázaro Cárdenas. So if that’s where you want to go it’s faster than going through downtown and you will see another side of Puerto Vallarta.
Busses going to points south, Mismaloya and Boca de Tomatlan, start from the South Terminal at Constitución and Basilio Badillo and the busses to El Tuito and other points south leave at Aguacate & Carranza. See Map

When you board the bus and pay your fare, no big bills, please.
Hold On ! a lot of busses will take off quickly, even while making change. Get to a seat as quickly as possible. Note: the two seats behind the driver, often painted yellow, are reserved for the aged, infirm or pregnant.
As you can see by the photo of the bus stop sign on the right some of the locals have quite a sense of humor.  

Walking

The non ‘tunel’ bus will go straight into town on Morelos, get of at any of the stops on this street and walk the one block down to the Malecón (seafront promenade). Stroll down this in the same direction the bus was going (south) and you will reach the Main Plaza, Town Hall and Church, see Map. If you continue south (or stay on the bus) you will cross the Rio Cuale and enter the 'south side' of town, lots of good restaurants, bars and coffee shops. Generally everything is cheaper on the south side of Puerto Vallarta. Go inland to see a typical local neighborhood or go down to the beach and have a drink down by the new pier at Langostinos, while you watch another incredible sunset.

The absolute best, and most economical way , to rent a car here is by booking on line before you arrive.  Best to book on-line Gecko Rent a Car, who, although they are in Bucerias, will pick you up at the airport. geckorentcar.com. it is the only car rental company I can honestly recommend.

Scooter/ATV

Real fun way to see the town. At Estigo Scooters you can rent Scooters - US$13 an hour. US$69 per day or even weekly. Or an ATV, a great way to get around on our cobbled streets, for US$32 an hour and US$89 per day.
Av.Francisco Villa 384-A, 2 blocks east of the Mega Store,
Tel 322-223-8143 Cell 044-322-100-9464 or Vonage US number 213-353-9665.

Taxi

City Yellow Taxis
From Downtown to the South		From Downtown to the North
Dreams Resort	60 pesos	Marine Terminal	60 pesos
Mismaloya	120 pesos	Airport	80 pesos
Boca de Tomatlan	140 pesos	Nuevo Vallarta	180 pesos
		RUI & Flamingos	220 pesos
Travel within one zone is 40 pesos

Vista Vallarta Golf Course from
Downtown	220 pesos	Olas Altas	250 pesos	Neuvo Vallarta	250 pesos

Marina to Nuevo Vallarta

160 pesos

Or 250 Pesos per. hour, but make a deal for a half or full day for less.

Before entering the taxi, ask the driver what the fare will be to your destination, if it isn't close to the guide lines on this page, go to another taxi. Tips are not required, unless you feel it is warranted. The local custom is not to tip, unfortunately many visitors do not know this and tip as they do at home, the result is that the locals have a hard time getting a taxi when they may urgently need one, the taxi will bypass them looking for a tourist who will tip them and pay more for the trip than necessary.
Tips from drivers on where to eat etc. are not reliable (they will be getting a kickback). There have been some recent complaints of taxi drivers taking people to different places than requested because of this. If the driver tells you the place is closed or he doesn't know where it is - take another taxi. If he takes you somewhere else anyway, find police officer - they all speak English, this will help us get rid of the bad drivers. Also taxi drivers may not know the street names. Even local residents don't know the names of the streets, I've had neighbors who didn't know the name of the street two blocks away. They do know places, I've been given directions like "Turn right on the street just past where the car wash used to be" So I suggest you print out my maps, each one has a printer friendly version.

 Airport Taxi

These special Federal licensed taxis are only allowed to service from the Airport to Hotels and Condos, more expensive than regular ones. 163 - 800 Pesos depending how far. Here's a guide, These rates are of August 2009.

Private Driver for the day.

Get a bilingual private driver with a air-conditioned van (capacity 14) for a mere $40 US per hour (4hr. min. in town only), includes a cooler with ice and drinks can be arranged. Go where ever you want to go with a very knowledgeable driver.
Pick-up from your hotel, casa, cruise ship or the airport.   Superior Tours

Bay Busses.

Are slightly longer route busses that can take you to some very nice beaches on the north side of the bay, beyond the bay and to El Tuito, a small town to the south that is older than Vallarta.

ATM (Autostransportes Medina de Puerto Vallarta) leaves it's terminal at Brazil #1410 (at the south side of the Sports Stadium), every 7 min. to Punta de Mita and every 10 min. to Nuevo Vallarta. The busses stop across from Copal (in front of HSCB Bank ), in front of Walmart and across from the airport. Look for the sign on the Maps.
The Nuevo Vallarta bus goes to all the hotels in Nuevo. To reach downtown PV you'll have to change from the ATM bus to a local one. The easiest place to do this is at the Marine Terminal (across the road from Walmart,Sam's), just get off there and wait for the next city bus going to 'Centro' - see top of the page for more info. on Local Busses.
Fares are Bucerías - 14 pesos, Nuevo Vallarta & Valle de Banderas - 14 pesos, Destiladeras Beach - 17 pesos and Punta Mita (El Anclote Beach) - 26 pesos.
The Compostela-Pacifico line (White & Green) has service to Sayulita - 26 pesos, and takes you to the Sports Stadium. It leaves from the same stops as the ATM Line, on the return the last stop is at Plaza Genovesa. The same bus line also has service to San Francisco (San Pancho) and Rincón de Guayabitos, but not into the towns themselves.

El Tuito. The bus to El Tuito leaves from the corner of V. Carranza and Aguacate, see Map. The fare is 20 pesos and takes about 50 min.
A nice excursion you can take for yourself to an old colonial town and a source for Raicilla. See Raicilla

South. The bus to Mismaloya and Boca de Tomatlan (water taxi to Yelapa) leaves from the corner of B. Badillo & Constitución and B. Badillo & Insurgentes, on it's way south.

Intercity Busses
Bus Travel Bulletin Board
These busses, many of them very luxurious, can be found at the Main Bus Terminal just north of the airport, Map, see this link with a nice plan of the place, including links to the bus lines. There are some places in town that you can book and purchase tickets in advance. One is opposite from Farmarcia Guadalajara on Insurgentes, between L. Cardenas and V. Carranza, where the photo on the right was taken. The busses to Manzanillo also stop for passengers on the corner of Aguacate and V. Carranza, The Cihuatlan,Pacific Line also runs 2nd class busses south. There's a lady on that corner that sells tickets, Mary, she has curly hair, usually reddish blonde, you can reach her on her cell at 044-322-138-8343 from a land line. or at home 223-2477, if you have any questions. Map.
First class service to Manzanillo: The Flecha Amarilla - Primera Plus Line has a First Class bus at 07:45. Web Site. The Chiuatlan - Pacific Line runs two Primera Plus Class busses per day, one at 16:00 (4:00 pm) and at 23:30 (11:30 pm). Lots more second class service: Flecha Amarilla - Servicios Coordinatos run Second class busses at 7:00, 16:00, 19:45 22:30 23:30 and 01:30 Cihuatlan,Pacific Line run second class buses at 05:00, 06:00, 07:30, 08:30 09:30, 11:30 12:30, 14:30, 15:30, 17:30 and 19:30 These are all bus station times. Web Site. Futura - also has some busses, see Web Site. Mazatlan can be reached in 6.5 hours, via Tepic on TAP for 320 pesos, regular service. Web Site ETN, the most luxurious bus line, leaves for Guadalajara at 00:30, 01:00, 07:45, 8:45, 10:15, 11:45, 13:00, 14:00, 14:45, 15:30, 16:15, 17:00, 24:00       ETN site is in English ! Another option in traveling to Guadalajara is 'Vallarta Plus", a line that takes you to their own terminus in Guadalajara - not the Bus Station that is not near the center of town. Map Only 276 pesos each way. The terminus here is on the right of the access road to the Central Bus Station. Map You can book your bus trip at Superior Tours located in Plaza Romy. L. Cárdenas and I. Vallarta. Map     Here're the fares
You can now travel the scenic route to and from Guadalajara, via Mascota and Talpa de Allende. Not a direct trip, you'll have to change in Mascota or Talpa. Three busses a day from PV with ATM Red Line to Talpa and nine buses a day from Talpa to Guadalajara. ATM Web site Red Line terminal on this Map.

 Water Taxi

Rosita Hotel Beach to Yelapa Beach 125 pesos + 10 pesos. for the boat from the beach to the launch. Expect getting your feet wet.

Los Muertos Beach to Yelapa 125 pesos 1st class pier to pier - no chance of wet feet, but a longer ride than above.

Or take a Taxi $10.00 (100 Pesos ) or Bus .50c (7 Pesos) to Boca de Tomatlan then water taxi from the beach.
Boca de Tomatlan to Las Animas, Quimixto, Yelapa 60 pesos or Pizota for a bit more. Prices vary sometimes.

Water Taxi Schedule for Yelapa from Boca de Tomatlan.

Water Taxi Schedule for Yelapa from Los Muertos Beach Pier. MAP

From David's Yelapa.info Site