No Wall Street analyst follows Apple’s (AAPL) retail operations more closely than Needham’s Charlie Wolf, who has been using quarterly in-store sales as a metric for how well the Apple Stores are doing in general.

But you can sense his frustration in a note to clients issued earlier this week in which he reports that in-store sales, while up sharply year over year in the quarter that ended Christmas Day, are “fluctuating wildly,” as indicated in the chart above.

“It’s becoming evident that quarterly same-store sales have become less than perfect measures of the financial performance of the Apple Stores,” he writes. “We plan to continue to report quarterly results. But we’re also going to report annual trends in same- store visitors and same-store Mac sales.”

What’s going on? Wolf explains:

The Apple stores accounted for 14.4% of the company’s worldwide revenues in December, up slightly from 12.6% a year ago. After reaching a high of 21.6% in the second quarter of 2008, the Apple Stores’ share of the company’s worldwide revenues has been generally declining. The obvious causes of the downtrend have been the acceleration in the sales of iPhones, which are sold through a network of international carrier stores, and sales of iPads, which are already sold in over 10,000 outlets just in the U.S. In this regard, it’s instructive to note that the Apple Stores’ share of worldwide Mac sales has held relatively steady at around 20% despite an increasing number of stores selling Macs, especially abroad.

Reflecting the frenzy surrounding new product launches, non-Mac revenues have been on a rollercoaster. The sharp decline in non-Mac sales from March 2006 through September 2007 chiefly reflected the wider distribution of the iPod. The rebound in 2008 was driven by the iPhone, which at the time was initially sold only in the Apple Stores and AT&T’s carrier stores. In addition, before the iPhone achieved widespread international carrier distribution, foreigners purchased a substantial number of phones to sell in gray markets, especially in the Far East. The subsequent decline in non-Mac sales in 2009 most likely reflected the introduction of the iPhone into 90 countries. The increase in the last three quarters followed the April 2010 launch of the iPad.

The dramatic fluctuations in same-store non-Mac sales calls into question the usefulness of this metric in assessing the performance of the Apple Stores. The fact that non-Mac sales in the Apple Stores are in a sense hostage to Apple’s overall distributions strategy limits its usefulness. More generally, quarterly numbers tend to obscure longer-term trends. Quarterly same-store Mac sales have fluctuated quite widely. But a portrayal of annual sales shows that they have steadily increased since the Apple Stores first opened, with the exception of the recession year in 2009.

See also:

• The magnetic draw of the Apple Store

[Follow Philip Elmer-DeWitt on Twitter @philiped]