“We don’t intend to make any money off the App Store,” said Steve Jobs back in March. “We’re basically giving all the money to the developers and the 30 percent that pays for running the store, that’ll be great.” (link)

But like the iTunes Store, which Apple (AAPL) claims to run at “just above break even,” but which probably generated $200 million to $500 million in profit for Apple last year (see here and here), the App Store could prove to be a nice little cash cow for Apple over time.

How nice? Ask two different analysts and you’ll get two different answers.

In a report to clients on Tuesday, Bernstein Research’s Toni Sacconaghi ran the numbers and concluded: “We don’t see revenues from the new Apps (sic) Store as meaningfully impacting Apple’s economic model.”

If the average iPhone owner buys two programs at $5 each (a generous assumption, he says, given that 50% of iPod users have never bought anything from the iTunes Store), Sacconaghi estimates that the App Store will generate at most $150 million in revenue from applications by the end of 2009 (vs. several billion from the iPhone overall).

Piper Jaffray’s Gene Munster, by contrast, ran the same assumptions through his model and got a very different answer: total App Store revenue of $780 million in 2009, of which Apple’s cut is 30%, or $234 million.

Why the difference? It stems primarily from the two analysts’ projections of iPhone sales, which lie on opposite ends of the Apple analyst spectrum.

Sacconaghi is on the low end. He believes that by end of 2009, the iPhone user base will be about 25 million worldwide.

Munster occupies the high end. In his note to clients he estimates the iPhone installed base at the end of 2009 will be 78 million users.

[Note: Since Munster's spreadsheet only models 61.6 million iPhones at that point, it's not clear how he got that total. Perhaps he is counting iPod touches in that total. Or more than one user per iPhone. We'll update when we get to the bottom of it.]