Well, I primarily use Strikezone
http://www.strikezoneonline.com/hero_clix.htm, They also list how many in stock, for instance: 5 @ $.36, 5@ $1.17, and 3 more @ $3.20 each, depending on experience level of the figure. They normally try to keep their stock up.
After Strikezone, I use The Gaming Store
http://gamingetcstore.com/heroclix.html, They list when they're out of stock, but not how many they have. A little more expensive at $1.49 to $3.99 each.
I know that there are other vendors that sell singles but these two seem to have what I need most of the time.
Some of the prices are ridiculous, though, because of a self inflated rarity! ($150.00 for a Green Lantern figure!)
SteveN