digital in you would be using an outboard ADC (analog to digital conveter) analog in your recording device (R-09) does the conversion for you. if you are doing low profile taping or are on a budget analog in can be nice as its one less piece of gear to carry around (unless you use a pre/adc combo in front)
many have commented that the ADC in the Edirol R-1 is very nice and it will likely be similar if not the same in the R-09.
when all is said and done its all about what sounds better to your ears. some will prefer the sound of a stand alone ADC others are perfectly content with using the ADC in their recording device.