Quoted from Whysnow:

It really depends on the game.
In some cases they are worth much less. Example of the whitewood Andromeda. It was cool to see it pop back up but sold for less than standard versions sell for. I attribute this to the fact that standard Andromeda has such great art that a whitewood takes away one fo the bets feaftures of the game. I think that whitewood has an additional feature of an extra drop, but it does not add to the game. A game liek this is already very rare so a sample/whitewood is not all that much more rare in relative comparison.
In other cases they are worth more. Example of TZ or other popular games where prototype often have added art and features, are still full featured, and in fact more rare than a large production run.
It really just depends.
There are some sample/proto games I would love to own and pay extra for.
There are others I have been offered for less and have passed on.