There's rarity, there's scarcity - and there's also demand. You could create the rarest deck imaginable, an issue of one, and if no one has heard of it or wants it, it has no worth whatsoever, except perhaps to the person who created it.
The toy craze was mentioned - and yes, there's a big market for collecting rare toys. But even there, the market has shifted. Whereas at one time in history, toys didn't last long because kids played with them 'til they fell apart, now more and more of these new toys coming out are being sought by collectors, who want the special collectors edition in the serial-numbered box and the bonus widget that comes in a special presentation box, etc. Those toys DO NOT GET PLAYED WITH terribly often. A handful might "escape" from their boxes because someone wants to display them on a shelf or something similar, but in general they're very well cared for. Thus, the attrition rate for such toys is low, so most of the ones made will still be available years down the road. Toy companies aim for a balance of quantity (so as to not anger collectors wanting complete collections) and rarity. Aim too hard for rarity and you make less money, unless you release a boatload of "rare edition" toys, in which case those completists get angry again, because it becomes too difficult to make a complete set.
There are some parallels here, but it's important to remember that in playing cards, there's nowhere near as much "mint-in-box syndrome" going around. Playing cards have been around for hundreds of years and have always been a popular game - there's almost no other game on the market that can be played with in so many different ways. There's some collectors who will buy them for the sake of owning them, like having bragging rights or something, but to me it's akin to paying good money for rare paintings and sculptures and either tucking them into a storage system somewhere, never to see daylight again, or put them on display while their still in their crates. Perhaps the crates are interesting sometimes, but you can't actually appreciate the art that way.
That's a big way in which playing cards vary from toys. A full-custom deck can be a thing of real beauty, much like a well-made toy sculpt, but while the toys tend to come in flashy packaging that shows off the contents in all its glory, playing cards in their box will at most display the front of one card, the back of another and the edges of all the cards - and that's no way to appreciate a work of art, now is it?
Vintage playing cards obtain their value for the same reasons as vintage toys - no one expected them to last forever, few people saved them, and in many cases the examples you do find are opened and well-used. A "mint-in-box" pack of any deck that's old enough has a significantly higher value, of course - and the point Tom made about the cross-appeal is important as well. Card collectors AND Coca-Cola memorabilia collectors will be looking for that cool pack of Coca-Cola playing cards, and Lewis Carroll fans will be just as eager as you are to get that Alice in Wonderland themed deck, etc., thus making the demand higher than it would be for a more pedestrian pack of cards.
I can't imagine that the "artificial rarity" of limited-run custom decks will make a great deal of cash in the long run, not unless the hobby of card collecting grows in leaps and bounds. The rarity is there, but many of us already get the decks we like, if not at the initial offering, then through eBay, trading, etc. If the demand suddenly shot up with new hobbyists, that would be the tipping point. There's no way to know if and when that will happen - it's something we fervently hope for, but at the same time something that we dread, because THAT'S when even garden-variety "collectors' decks" will start becoming really scarce and prices will go up not only for our collections but also for all the other decks you don't have yet but really want someday! Vintage/antique collectors will feel the pain first, because there you have cards that were never meant to be scarce in much the same way that they were never meant to last all these years - they weren't scarce by design, but are so anyway, and good examples can be difficult to find - any not already in collectors hands may be deteriorating as we speak, sitting in a drawer in that dresser in the back of the garage that crazy old guy owns, next to the rats' nest that needs bedding material...