I have received several PM's recently asking newbie-type questions about the taxis in San Jose and Quepos/Manuel Antonio. Here's a basic overview of the taxi situation in costa Rica.
1. Licensed taxis will have a sticker on the door, a yellow triangle with the cab's number on it. This lets you know that the cab is licensed and is equipped with a (probably) working taximeter. Pirate taxis, unlicensed cabs will not necessarily save you any real money, although sometimes late at night a pirate cab will be easier to find.
2. When boarding the taxi, politely ask: "Ponga la maria, por favor" (Put on the taxi meter, please). Watch the meter yourself.
3. Carry coins, as the drivers seem to never have change. You'll find 500 and 100 colones coins especially useful
4. Tipping is not expected, although I always just rounded the fare up to the nearest 100 colones. (i.e. I would give a cabbie 700 colones for a 640 colones fare).
5. The orange taxis from the airport to your hotel charge a predetermined price of $12.00 U.S.; may be more if your hotel is far to the east of downtown. You should purchase a prepaid taxi ticket at the little booth immediately to your left as you exit the baggage claim/customs area at the airport.
While we're on that subject, watch out for the guys who pretend to be sky caps hanging around the taxi queue. These are not airport employees; they will take your bag from your hand and load it into a taxi a few feet away, and then demand a tip of around $2.30 (1,000 colones). You are under no obligation to allow anyone to touch your luggage, and certainly have no obligation to tip.
6. Do not take a taxi from immediately outside the BM/KL; those thieving bastards will overcharge you by nearly double.

Instead, walk down a block and around the corner, hop a licensed cab and ask the driver to "ponga la maria, por favor."
7. Despite the fact that all licensed cabbies have to take a street geography test in order to obtain their license, most drivers are absolutely clueless (or pretend to be) about the location of many places discussed here on CRT. A map, such as Get Rhythm's excellent map of the Gulch available elsewhere on this site, will help guide the cabbie.
8. Do the drivers speak English? Chances are, no. Several drivers we encountered right in the Gulch spoke some English; many seemed to understand more English than they speak, but it will certainly help to either speak some Spanish, or be able to pass the driver a written note with typical tico directions on it:
"200 m. oeste de edificio INS" will be more useful than saying, "At the corner of calle 3 and avenida 7" for instance. remember that cabbies in SJO use landmarks, not street coordinates.
8. Never, never allow the cabbie to suggest a strip club or massage parlor. One favorite tactic of less-honest taxistas is to pretend not to be able to find the club you want to visit, taking you instead to another club. They do this to earn commissions from the clubs/MPs. This is a growing problem.
Another tactic to be aware of is the orange taxi drivers who will tell you that your hotel is rat infested, burned down, closed by the health department, etc. They will then happily take you to an alternate hotel, one which pays them a commission. Don't fall for this shit.
9. Cabs are no guarantee of safety, unless you lock your door and/or close your window. Thieves in C.R. have been known to reach in through the window of a stopped taxi and tear the necklace right of the tourist's neck. That being said, it is much safer to take a cab around el centro at night than to walk it, and it's not expensive.
10. Typical cab fares in and around the Gulch will range from 400 colones (less than a buck) to 1,000 (for very long trips). Five hundred seems to be typical, say from the Sportsmen's Lodge or Hotel Castillo to the BM.
Hope this helps. I am a non-driver who takes cabs wherever I travel, and I have found the taxis in SJO to be very reliable, mostly clean and a very good value if one follows the ten suggestions above.
A note on taxis in Quepos / Manuel Antonio: Most cabs in this area are not equipped with meters, so negotiate a fare before boarding the cab. We found cabs on the Pacific coast to be about 20% more expensive in general than those in San Jose, but YMMV. It is possible almost anywhere to hire a taxi and driver for longer trips/longer periods of time. One Quepos driver offered to drive us to San Jose for $80.00 (fairly high price).
Happy motoring!
