i386 and i686 refer to the processor architecture. Intel 386 is a 808386 (actually I'm not sure fo the complete name) processor (aka 386). The i686 refers to a PII (or K6) and upwards (I think), since there hasn't really been any difference in the chips except for the speed since the MMX instructions back in the days of PII.
It doesn't really matter which one you choose, as long as it isn't PowerPC, ia64 or x86_64.
