Piper Jaffray analyst Gene Munster has upped his estimate of the number of iPhones he expects Apple to sell in its 4th quarter, from 4.1 million to 4.47 million, according to a report to clients issued early Wednesday.

In the same period last year, Apple (AAPL) sold 1.12 million first-generation iPhones.

Munster’s new estimate is based 1) on Apple’s report that it sold 1 million iPhone 3Gs in the three days following the device’s July 11 launch and 2) on 25 hours of in-store checks across the United States conducted over the past two weeks.

His team counted sales in both flagship and “regular” Apple stores and concluded that Apple sold an average of 95 units a day in each of its 188 U.S. stores over the next 27 days. He combined these results with estimates of the number of iPhones sold at AT&T’s 2,200 outlets and the number sold by overseas carriers to get a grand total of 4.47 million.

On Tuesday, Fortune.com reported on the findings of an independent analyst, Michael Cote of the Cote Collaborative, who estimates that 3 million units were purchased worldwide during the iPhone 3G’s first 30 days on the market. (link)

Piper Jaffray’s estimate is probably conservative, says Munster, because it doesn’t take into account iPhone sales in the 22 additional countries scheduled to start carrying the iPhone on Aug. 22. Moreover, he reduced to 31 his estimate of the number of iPhones sold per day for the remaining 51 days in the quarter, which ends on Sept. 30, based on a 10% falloff in sales his team observed between the first week of observation and the second.

The charts below summarize his findings:

In a move that will significantly expand its retail presence in time for the holiday season, Apple has agreed to let retailing giant Best Buy sell the new iPhone 3G through its nationwide chain of Best Buy Mobile outlets starting early next month.

Best Buy markets cell phones in the United States through 970 full-size stores and 16 stand-alone Best Buy Mobile shops. All U.S. Best Buy stores will carry the iPhone except for a handful of outlets located in areas where AT&T does not provide cell phone coverage.

The deal, first reported on Tuesday by Apple Insider and confirmed by Best Buy Mobile president Shawn Score (see here), could serve both companies well.

For Apple (AAPL), which has been struggling to meet the extraordinary demand for its second-generation iPhone through its smaller network of Apple and AT&T retail stores, the deal puts its hottest-selling product in the hands of one of world’s savviest retailers. Best Buy, a Fortune 100 company, is the world’s largest consumer electronics retailer, with a 21% share of the U.S. electronics market and a 3.6% share of the cell phone market, up from 2% last year.

For Best Buy (BBY), which has been angling for the iPhone business for more than a year, the deal will add Apple’s cachet to its expanding smartphone offerings and help drive traffic to new Best Buy Mobile departments within its stores. Best Buy is aggressively marketing a variety of smartphones, from RIM (RIMM) BlackBerry Curves to Palm (PALM) Treos, and is the exclusive reseller, with Sprint (S), of the Samsung Instinct, one of the iPhone’s nearest competitors.

Apple and Best Buy have been slowly expanding their relationship since the retailer began carrying iPods in 2002. Best Buy started selling Macs in selected stores in 2006, and recently expanded the program to more than 600 outlets.

The deal can be seen as a victory for Best Buy’s “consumer centricity” marketing strategy, by which it caters to the needs of specific types of customers in specialty boutiques within its full-size stores. Last week Best Buy announced that it had completed a nationwide roll out of its Best Buy Mobile store-within-stores, a joint venture with Britain’s CarPhone Warehouse that began in 2006 and has led, according to Best Buy, to a 10-fold increase, year-over-year, in high-end multimedia phone purchases (link).

Best Buy, based in Richfield, Minnesota, operates more than 1,150 stores in the United States, Puerto Rico, Canada, China, Mexico and Turkey. Earlier this year it purchased a half-share of CarPhone Warehouse, which has 2,400 outlets in nine European countries.

Apple operates 219 stores, 187 of them in the United States, where customers have been queuing up for the iPhone 3G since early July. AT&T (T) sells iPhones in some 2,000 stores, but the current waiting period for customers who want to buy one from AT&T is 7 to 10 days.

It’s been a month since the iPhone 3G and the App Store made their debut, and Steve Jobs used the occasion to offer up some selected facts and figures:

• Users have now downloaded more than 60 million programs for the iPhone and iPod touch, or roughly 2 million per day.
• Revenue from those applications came to about $30 million. 70% went to the developers; Apple kept 30%. (Free apps apparently accounted for the vast majority of the downloads, since average revenue per download is 50 cents.)
• If sales continue at the current pace, Apple stands to clear at least $360 million a year. “This thing’s going to crest a half a billion, soon,” Jobs told the Wall Street Journal. “Who knows, maybe it will be a $1 billion marketplace at some point in time…. I’ve never seen anything like this in my career for software.”
• Of the $21 million that developers cleared in the first month, roughly $9 million went to the creators of the top 10 best sellers. Sega Corp., for example, says it sold more than 300,000 copies of its $9.99 Super Monkeyball game in 20 days.
• Jobs believes a rich array of applications is what will distinguish the iPhone from competing cell phones. “Phone differentiation used to be about radios and antennas and things like that,” he told the Journal. “We think, going forward, the phone of the future will be differentiated by software.”

Apple had earlier reported that 10 million apps were downloaded in the first three days after launch. By July 21, that number had reached 25 million (see here). The latest number suggests that downloads have accelerated in the last 10 days, from July 21st’s 1.25 apps per day to the current 2 apps per day.

Relations between Apple (AAPL) and its developers have not been smooth, however (see Trouble in the App Store). Jobs commented on one of the hot-button issues: He confirmed that the iPhone operating system contains a kill switch that gives Apple the capability to reach into an iPhone (presumably during a sync operation) and remove a malicious application.

“Hopefully we never have to pull that lever, but we would be irresponsible not to have a lever like that to pull,” he said.

Separately, an Apple spokeswoman defended the decision to pull a program called I Am Rich, which cost $999.99 and did nothing but display the image of a ruby on the iPhone’s screen, off the App Store shelves. She characterized it as a “judgment call.”

Jobs did not use the occasion of the iPhone 3G’s one-month anniversary to report how many of the devices Apple has sold. He may be saving that number for another day — and another round of headlines.

[Fortune's Scott Moritz reported Monday that at least one analyst puts iPhone sales for the first month at 3 million units. See here.]

UPDATE: Gigaom’s Om Malik, who says he has downloaded three dozen apps but only likes four of them, adds some interesting data about how many of those 60 million apps are in active use. He cites research by New York-based Pinch Media, which reports that free downloads to paid downloads is about 10 to 1. Moreover:

“According to data collected by Pinch Media, on average, less than 20% of an application’s overall unique users return to an application each day. [CEO Greg] Yardley also pointed out that people are using the apps for just under five minutes at a time, on average. The majority only use the applications once per day - average number of uses per day is around 1.2.” (link)

It’s been a confusing week for both sellers and buyers at the App Store — the venue for third party software that is the best thing to happen to the iPhone (except maybe the price cuts) since it arrived more than a year ago.

The iPhone 3G is OK, if you manage battery consumption very carefully. And Mobile Me is slowly getting up to speed (see here). But the App Store — with 1,574 programs as of Saturday morning, from Abacus to Zxilophone — is a runaway hit, a software candy store that offers iPhone and iPod touch owners a fresh tray of tasty treats nearly every day.

So what are we to make of the fact that Apple (AAPL), without explanation, has started pulling programs from the store, leaving both the people who wrote them and the customers who bought them scratching their heads and wondering who’s in charge? At least five apps have disappeared so far, but three dominated the tech news this week:

• BoxOffice: This free application, which listed movie times, locations and links to reviews, was one of the first programs available when the App Store opened on July 11 and offered worthy competition to Movies.app, a must-have program from the early days of the original iPhone. BoxOffice disappeared from the App Store on July 31. “Apple pulled the app yesterday without giving my (sic) any notification that they were doing it, or what their justification was for removing it,” its developer, Metasyntactic, wrote the next day on a MacRumor forum. “I’ve tried to contact them about the issue, but it’s been a complete dead end. If anyone has a useful contact number for apple, please let me know.”
• I Am Rich: This one is a little easier to understand. The priciest app in the store — it sold for $999.99 — was also the most useless: it did nothing but take your money and display a red gem on your screen. “The red icon on your iPhone or iPod touch always reminds you (and others when you show it to them) that you were rich enough to afford this,” the information page on iTunes warned. “It’s a work of art with no hidden function at all.” Apple, which was collecting $300 for every copy that sold (and at least eight did, developer Armin Heinrich told Silicon Alley News), may well have received complaints and felt obliged to protect unwitting customers. But what kind of screening process approved I Am Rich in the first place?
• Nullriver: This may be the most bewildering case of all. The application allowed Mac owners to use their iPhone as a wireless modem to reach the Internet over AT&T’s (T) cellular networks — either 3G or EDGE, whichever was available. It was removed from the store on August 1, briefly reinstated, and then pulled for good. According to Nullriver CEO Adam Dan, technicians at Apple told him it was pulled the first time by mistake. “They want to get NetShare back up, but they want to do some technical analysis that they couldn’t explain to us,” Dan told Wired.com. As iPhone Savior pointed out at the time, AT&T’s user agreement clearly forbids unauthorized tethering (see here), but it’s not clear why AT&T would object to the extra revenue stream. “Apple runs the app store, so you’ll have to ask them about the availability of this and other apps,” an AT&T spokesperson pointedly told Gizmodo. “For customers looking for a smartphone with tethering capabilities, AT&T has a number of other options to choose from.” Perhaps it was Apple that had a problem with Nullriver. They may have their own tethering plan in the works, and Nullriver might well have offended someone in Cupertino’s sense of how easy-to-use an iPhone app ought to be (tethering is never easy, and the instructions included in Nullriver were hopelessly inadequate.)

Apple has not responded to requests for comment, so nobody really knows for sure what’s going on. But it sounds like they were overwhelmed by the initial flood of applications and may be trying, by fits and starts, to develop a rational policy.

“From what I can tell their approval process is not very strict at all,” Nullriver’s Dan told Wired.com. “I think they run it, start it up and if it doesn’t crash they approve it. They brainlessly click through, and if there’s problems they remove it.” (link)

Even more troubling, for some observers, is the discovery of what seemed to be a blacklist mechanism buried in iPhone OS 2.0 and unearthed last week by Jonathan Zdziarski, author of iPhone Forensics. It consists of an URL that points to a page of unauthorized programs.

“This suggests that the iPhone calls home once in a while to find out what applications it should turn off,” writes Zdziarski. “At the moment, no apps have been blacklisted, but by all appearances, this has been added to disable applications that the user has already downloaded and paid for, if Apple so chooses to shut them down.”

For an extensive discussion of the significance of this list, see Techmeme here.