Latencythroughput. While each is a measure of speed in some sense, they are not exactly the same thing. Latency is a measure of amount of time between the start of an action and its completion, whereas throughput is the total number of such actions in a given amount of time.
To illustrate, let's compare the transatlantic flights of a jumbo jet airplane and a supersonic passenger jet. The jumbo jet carries 1000 passengers but each trip requires 10 hours, while the supersonic jet is limited to 50 passengers with a flight time of only 2.5 hours. In this example, the jumbo jet effectively transports 100 passengers each hour it is in flight (throughput), but every passenger is stuck on the plane for the full 10 hours (latency). In contrast, the smaller plane averages only 20 people each hour, but those people enjoy a much shorter trip.
Both latency and throughput have a dramatic effect on the design of telecommunications and computing systems, because improvements in one aspect often come at the expense of the other. For most operations, such as transferring files on your computer, throughput is the most important measure, because such operations aren't complete until all of the data has been transferred. On the other hand, the control system for the brakes on a car only needs to send a little bit of information (on or off), but that information needs to be sent with the shortest delay possible.
In biology, latency also refers to the period of time between the application of a stimulus to a muscle cell and the actual contraction of the muscle. This occurs while the sarcolemma (the outer covering of the cell) is becoming more positively charged (depolarized).
For computer music, latency is extremely important. A human playing an instrument, for example, needs nearly instantaneous feedback from that instrument in order to play it correctly. While this is not a problem with non-digital instruments, devices connected to a computer always have some delay in the signal path. Latencies higher than 100 ms generally make working with real-time music programs or instruments impossible.
Out of the need for low-latency interconnects, Steinberg created ASIO, a protocol designed for low-latency transmission (on the order of 1-2 ms) of digital instrument and other music data. Recently, out of the desire for a free solution, people created JACK Audio Connection Kit, a piece of software that also provides for latencies like 1 ms.
See also rotational delay, which is another form of latency.