A Castlevania 64 prototype recently sold for over $500 on ebay. As the seller described, there were no discernable differences in the gameplay, glitches, etc. It was simply titled "Castlevania Prototype," so it's solely up to the seller & buyer to determine if that specific designation makes it valuable enough to warrant such a high price tag.
I suppose the same can be applied to your prototypes. In my personal opinion, these types of things should be going for no more than $100 UNLESS they contained something unique that the standard public release does not (altered graphics, missing/added effects/enemies/items, etc.), but this usually applies to BETAS, as opposed to prototypes. As uzo said, betas & prototypes are 2 different things, 1 being worth more than the other on the market, depending on the details. Sadly, not everyone is aware of this.