Some cards are priced at regular retail, though most shops offer some sort of show discount. But generally, prices are still high - common set singles from 50 yen (occasionally 30 yen), inserts start at 100 yen (the usual 200-300 yen for this year's cards), and parallels and autographs tend to start around 500 yen. There are 100 yen boxes where decent deals can be found, and I've occasionally had a great find in a "discount" box. But still, prices aren't anywhere near US dime boxes. (Oh, how I miss those dime boxes.)
By the way, some of you already know that there are proxy services to buy from YJA while living in the States, though they aren't cheap. If you do live in Japan, setting up an account is a must, and no credit card is necessary - in the past I paid using the Japan Post Bank, and Yahoo now has a free easy payment service where you can pay at convenience stores in cash!