Bimma's response was actually a lot more on target than mine so I'll elaborate ~
# of inputs shouldn't be more than two (on a non-DVD unit) if that many, I wouldn't think? A brand-proprietary input for CD changer or other same-brand gear and an RCA for auxiliary audio input would be it for most units that have any at all.
Differences (and differences in pricing) will result from number of preamp outputs and the output voltage that they are rated for, S/N ratio on the tuner and CD sections, resolution for the D/A converter(s), internal amplifier output, display information/picture capability, how involved the internal crossover network is (or isn't) if there's one at all, etc, etc, etc.
The main difference in price, however, will be the differences in the internals used to build each respective unit. There's a reason that the top-end Jensen/Dual/Audiovox/etc and the top-end Eclipse/Alpine/Premier/etc have a vast difference in price. The latter group simply make better decks than the former group. Better in quality, reliability, and overall sound.