As others mentioned, a 3 channel amplifier has three separate channels or amps on board. This would be handy for example when powering your front stereo pair plus a center channel speaker. Then you could power your surround channels with lesser amplification (maybe the part build in to an A/V receiver) since those are less demanding than the 3 front speakers.
I have used a 3 channel Parasound amp at some point, just to power a stereo setup with no center channel. It works fine. You are obviously "wasting" the circuitry in that center channel but if you find a good deal on a good amp, it might still be worthwhile.