Deutsche Bank’s Chris Whitmore did his homework last weekend.

First he waited in line for nearly four hours at Apple’s (AAPL) flagship San Francisco store to buy his own pre-ordered iPhone 4 (“Apple provided lunch and bottled water which was unexpected and well appreciated,” he says). And then he and his colleagues contacted more than 100 U.S. and European retail outlets over the weekend to gauge just how fast the things were selling.

The results of their survey were released in a note to clients Monday morning. According to Whitmore, 60% of Apple Stores were sold out by the end of launch day Thursday, as were 100% of the retail-partner stores he and his team contacted — Best Buy (BBY) in the U.S., O2 and Car-Phone in the U.K., and Orange in France.

Apple was able to replenish some supplies overnight, but by the end of the day Friday, there were stockouts at 80% of Apple Stores, 90% of O2 and 100% of the Best Buy and Orange retail stores. By then, even the Apple Stores were having trouble getting new supplies, and by Saturday, only 5% had iPhones in stock.

“We believe initial weekend volumes were 1 million plus,” he concludes. “But shipments could have been dramatically higher if there was more supply.”

What’s the secret of Apple’s success? According to Whitmore:

“We view Apple’s large and rapidly growing iOS installed base and iTunes / App store as the competitive moat which competing handset vendors cannot replicate. As highlighted [in the chart at right], there are ~235K apps available on the iTunes App Store which is growing at a rate of 10-20% M/M. In addition, cumulative App downloads exceeded 5B in June 2010 (vs. 4B in April 2010, 3B downloads in January 2010 and 2B in September 2009). By comparison there are approximately 61K Android Apps (although this platform is forking for various implementations) and 8K Blackberry Apps. We continue to view the App Store and Touch UI as primary sources of long-term competitive advantage for Apple.”

He thinks his new iPhone is pretty cool too.

“In aggregate,” he writes, “the line was long but not overwhelmingly painful and getting to play with the new toy was worth the effort. In addition, contrary to blog postings of calls being dropped we found AT&T cellular service on Friday was roughly same as pre- iPhone 4 coverage and we had no problems with the new external antenna.”

See also:

• 77% of iPhone 4 sales were upgrades
• First day sales: 1.5 million iPhone 4s?
• What’s driving iPhone 4 sales
• What the iPhone means to Apple

[Follow Philip Elmer-DeWitt on Twitter @philiped]