For nearly three years the professional sell-side analysts who cover Apple (AAPL) for the big banks and brokerage houses got clobbered every quarter by a motley group of amateurs — bloggers, day traders and individual investors who bet on Apple to beat the Street’s consensus and hadn’t been wrong yet.

But the indies’ luck ran out last October when they came in high and Apple came in low. They beat the professionals one more time in December, scored a draw in April, then lost in July and once again last night.

When the pros outgun the amateurs three times out of five, you have to wonder if some of them might know what they’re doing.

The big winner this quarter was Canaccord Genuity’s T. Michael Walkley, whose estimate for Apple’s bottom line ($9.67) was right on the money and whose forecast for iPhone unit sales (26.92 million) was pretty darn close (actual sales: 26.91 million).

Special mentions also go to:

• Evercore’s Robert Cihra, who came in first in the all-categories ranking by not missing any by much and by guessing the Mac unit sales number to within 10,000 units.
• Raymond James’ Tavis McCourt, whose estimate for Apple’s top line result ($3.939 billion) missed the actual result ($3.966) by 0.16%
• RBC Capital’s Amit Daryanani, who came in second after Walkley on the strength on second- or third-best guesses on Apple’s top and bottom lines.
• The Braeburn Group’s Luke Kittell, the only independent analyst to take first place in a major product category by lowering his iPad estimate Wednesday to an even 14 million.

The parade of bad guesses would have been even longer if we hadn’t eliminated from this quarter’s Earnings Smackdown any analyst who didn’t revise his or her estimates after  Tuesday, whenTim Cook signaled that iPad sales would come up short. But there were still plenty of bad guesses. Among the worst:

• Independent Navin Nagrani, who came in first place in Q1 2012 and dead last this quarter. His estimate of 32 million iPhones threw his whole game off.
• The Braeburn Group’s Ovi Popescu, who stuck with an estimate of 19 million iPads even after Cook’s warning.
• Sterne Agee’s Shaw Wu, whose estimate of 7 million iPod sales was off nearly 1.7 million units (31%).
• Bullish Cross’s Andy Zaky and Daniel (“Deagol”) Tello, two veteran independents whose gross margin estimates (43.5%) were 350 basis points too high.

Robert Paul Leitao, who supervised the expansion of independent Apple analysts, first at the  MacObserver’s (now defunct) Apple Finance Board, then at The Braeburn Group, plans to limit next quarter’s Braeburn participation to 20 members.

Below the fold: Our annotated master spreadsheet, with the best estimates highlighted in bright green, the second and third best in light green, the worst in red and the second and third worst in pink.