It started as a week-long “sprint project” — a bit of bare-bones entertainment for Apple’s (AAPL) iPhone, written as quickly as possible and published last January.

Within hours, users were complaining on the Internet that the game — which involved bumping off tiny island dwellers by flicking them into the water or launching them toward the sun, with no way to score points or win anything — wasn’t worth the 99-cents they paid for it.

Surprised and little hurt, its creators — programmer Dave Castelnuovo, 40, and graphic artist Allan Dye, 39 — promised to put out a new version. Which they did the following week, incorporating some of their users’ suggestions and sending it back to Apple for approval. They did it again the next week. And the week after that, for 14 weeks straight.

Thirty updates later, Pocket God is not only a perfect example of something sort of new — user-directed software development — but one of the best-selling programs on the App Store.

The game, once so simple, now surprisingly deep, has a dedicated army of followers who have purchased, at 99-cents a pop, 2.1 million copies and 180,000 add-ons (things like dance moves for the pygmies or new skins for the dinosaur). Kids as young as 3 play it, but the sweet spot of the Pocket God demographic seems to be 9 to 15, often male. You can see them yourselves. Just do a search on YouTube, where the fanboys (I think that’s the word) have posted countless cheats, bug reports and little pygmy narratives.

On Wednesday night at Macworld, Dye and Castelnuovo learned that their creation had been voted the Best App Ever, the top prize in month-long, 302,880-vote contest run by Jeff Scott, the man who monitors 140,000 iPhone apps at 148Apps.biz.

For the guys, however, it’s always been about having fun.

The two met in the early ’00s when Allan was doing animation for Cisco (a educational game called Peter Packet designed to teach 10 year olds how the Internet works) and Dave was writing the fly-over algorithms for World Golf Tour. When Apple released the iPhone SDK (software developers kit), Dave was keen to try it out, and he invited Allan to help him bang together a game in the week between Christmas and New Year’s 2009. They’ve been working together ever since.

“I’m the guy who dreams up even more sadistic ways to torture pygmies,” says Castelnuovo. “Allan’s role is to pull it back.”

But not too far. Among the myriad ways the islanders have been dispatched: drowned, skewered, eaten by sharks, hit by lightning, stripped to the bones by red ants, frozen to death, burned by a magnifying glass, roasted on a fire, fed to piranhas, blasted by a laser-carrying shark and ripped apart by an octopus.

In the most recent version of Pocket God, users have been given the power to change the temperature of the world — with mortal effects — by shrinking or expanding the size of the sun.

The users love it. The game was No. 1 on the App Stores bestseller list for a month last March. It’s drifted on and off the charts since then, but Dave and Allan have grand plans to keep the franchise alive. They’re making a version for Verizon and a couple spin-off games for the iPhone. They’ve sold the rights to a comic book based on Pocket God to Ape Entertainment (the publisher who made the Shrek comics for DreamWorks). They’re thinking about a line of Pocket God toys and, of course, what the game would look like on the iPad’s 9.7-inch screen.

Castelnuovo likes to compare what he calls the “Pocket God universe” — the characters, the art style, the sense of humor — with what Nintendo has with Mario and Sega with Sonic the Hedgehog.

But he recognizes that even with their 70% take (Apple keeps 30%), those 99-cent purchases only go so far — especially at tax time.

“People look at 2 million copies and go, you guys are millionaires!” says Dave. “But, uh, no.”

You can buy the latest version of Pocket God on the App Store here (updates are free). Go to CNNMoney.com for a gallery of the nine best iPhone apps, or see the full list of winners in all 56 categories at bestappever.com.

[Follow Philip Elmer-DeWitt on Twitter @philiped]