A friction clutch and a gearbox makes a very efficient transmission (i.e. very little power is "lost" in the transmission). This system is relatively simple for a driver to control manually using a clutch pedal and a shift lever. A torque converter by comparison creates more power loss. This fact, along with the simplicity and robust nature of the design, are reasons that a manual transmission uses this arrangement.
Why then do automatic transmissions use torque converters and planetary gears if they're less efficient? They're a cheap-to-produce and simple means of achieving automatic shifting, and the shift action they produce can be very smooth (i.e. no "lurching" during gear changes). They typically operate on a hydraulic control system that selects gears based on vehicle speed and accelerator pedal (or throttle) position. Howstuffworks.com has a great, in-depth discussion of how this control system works. Basically, this arrangement was used because at the time it was developed, it was the cheapest and simplest way to acheive automatic shifting.
With advances in technology, it has become possible to create an "automatic" transmission that uses a friction clutch (or commonly more than one friction clutch) and a "conventional" gearbox (e.g. BMW's SMG and M DCT, VW/AUDI's DSG, Porsche's PDK). These are often referred to as "manu-matic" gearboxes or "dual clutch transmissions". These combine the efficiency of a manual transmission with the convenience of an automatic, but the control systems and hardware required are far more complex than a "conventional" torque converter automatic, so these transmissions have not yet largely replaced "conventional" automatics.