You have four or five choices in public transportation within the city, depending on when you´re leaving from and how far you plan to go. Naturally there are lots of taxis, and these are the most expensive and (usually) most comfortable option. But lately there has been an increase in kidnappings by phony taxistas, who ransom their captives to earn a living. So I generally avoid taxis unless I´m in a really big hurry to get somewhere, or unless I know the driver.
If you´re just hauling a lot of groceries from the market and don´t want to carry them home on foot, you can take a moto, which is a motorcycle converted into a two passenger taxi. I´m told that it is a Peruvian invention. Since these are relatively slow vehicles, they don´t venture very far outside the neighborhood, except in rural areas where they are sometimes the only option.
If you want the comfort of a taxi but not the expense, you might be able to take a collectivo, depending on where you´re going. These are regular taxi cabs that travel fixed routes in the busiest areas, and charge a lot less than a taxi and about double what the buses charge. So if you are willing to walk a couple of blocks to a location where they pass by, this is often a very good choice, especially if you are in a hurry. Once they fill up with four passengers, they don´t make any stops until someone wants to get off.
At the opposite end of the expense/comfort spectrum are the combis, no larger than an extended minivan, which generally have three rows of seats behind the cab, plus a row of thin seats facing the opposite direction just behind the cab. When all the seats are full, they continue to stop for any potential passenger and try to stuff as many extra people in as possible. But they´re the cheapest way to get around.
On some routes there are full-size or medium-size buses. These are usually more comfortable than the combis and charge about the same. So they´re always preferable to a combi when one is available.
Interurban routes are served by three different classes of buses. The least expensive are crowded and offer no services. The tourist class buses have lots of leg room and generally have a toilet. They sometimes have two levels, with seats that convert to beds in the bottom level. The most expensive class of buses have air conditioning and heating. As far as I can tell, none of the drivers observe the speed limits or the double yellow lines on the highway.
I think one of the most difficult jobs in Lima is that of the cobrador, the driver´s assistant on a bus or combi who tells the driver when someone wants to get on or off, collects the fares, makes change, keeps track of who has paid and who hasn´t, and throws people off the bus when they become unruly or attempt to steal from someone.