I was under the impression that FLCL only had something like six episodes. Why's the box set so expensive?
FLCL was originally released by Broccoli's anime division Synch-Point. In 2008 Broccoli officially pulled out of the anime distribution business in America (and also pulled out of manga at the same time
) They released one full collection of the anime: a collector's edition with a t-shirt priced originally at $90. This is virtually impossible to find now due to less then one year of printing. The individual DVDs were put out of print twice before the company pulled out. By the release of the collection they were virtually sold out everywhere. Those were priced at $30 each (3 of them).
The anime's airing on advlt swim greatly increased the anime's popularity, which led to the stocks selling out so quickly, greatly increasing the value of those few on the market. I've seen them go for as much as $250 before. Poor saps were probably twisting in their seats when they heard FUNimation relicensed it, on blu-ray no less.
The most rare anime that I am aware of, though, remains Cardcaptor Sakura. I've seen that series go for $500+, a highly prized item that almost instantly went out of stock everywhere after Geneon pulled out.