As a collector who uses very few of his knives, I prefer to buy knives w/the box and any other material that came w/it. I sell very few of the knives I've purchased but, when I do, it's always better to have the box (and anything else that originally came w/it) than not.
However, I have purchased knives w/o a box if the knife itself is in excellent condition and it's a knife that I want and haven't been able to find elsewhere. It just depends.
I'm really not sure how the existence/condition of a box affects the sale/resale price of a knife.
I personally will NOT pay more for a knife than I think it's worth (regardless if there's a box or not) but I may NOT buy the knife at all if there is not a box (in reasonably good condition - not necessarily perfect) that comes w/it, if I can buy another knife in similar condition for the same (or a lower price) that comes with one.
Boxes are also better to have than not because it is easier to store/stack and organize the knives in boxes than when they are loose.
As someone else noted above, the boxes also have useful identifying information on them and, although I do not store all of my knives in their boxes, when I die, it will provide information to my executor that will help him/her match the knives w/their respective boxes in order to identify and price them before distribution or liquidation of the collection.