Over the last couple of days we’ve looked at which stocks are favorites of the Pros and which stocks were being added to Pro portfolios in higher-than-expected numbers during Q3.  Many of the stocks we mentioned were quite familiar, blue chips that make up the foundation of most Pro portfolios.  But what if we restrict our universe of stocks to small caps, stocks with a market cap of less than $1 billion?

Excluding ETFs, the most widely held small caps include Walter Industries (WLT), a diversified firm with interests in energy and homebuilding, REIT ProLogis (PLD), oil and natural gas producers SandRidge Energy (SD) and EXCO Resources (XCO), and chemicals maker WR Grace (GRA).  Looking at the small caps most added by Pros during Q3 shows several of themes names near the top of the list, along with oil and natural gas driller Grey Wolf (GW) and security services firm Brink’s (BCO).

Yesterday, we looked at the top holdings among the Pros at the end of Q3, and Johnson & Johnson’s (JNJ) eclipsing of GE (GE) in the top spot.  The names that occupy the top of that list are pretty predictable and have long been favorites of the Pros, but digging deeper we can find some names that appear to be getting more attention from the Pros.

Taking a look at the stocks where the most Pros were either adding to or initiating positions during Q3, we can see the usual blue chip suspects occupy the top of the list, but a little further down are some more interesting names.  Philip Morris International (PM), 32nd most popular among the Pros, was 16th most added by the Pros during Q3.  The “A” shares of Petrobras (PBR.A), 49th most popular among the Pros, were 26th most added by the Pros during Q3.  Biotech giant Amgen (AMGN) was another big mover.  It was 52nd most popular overall among the Pros but 37th most added.

With essentially all the Pro portfolios from the end of Q3 now available at tickerspy, we can head on over to Ideas & Research and take a look at what the data is telling us.

We noted recently that GE (GE) had overtaken Apple (AAPL) as the most tracked stock among tickerspy members.  Among the Pros, however, GE has been slipping.  It had previously been the top stock, but at the end of Q3 Johnson & Johnson (JNJ) became the top Pro stock (by just one, so it’s possible that any late filing Pros will throw GE back in to the lead.)

GE is the bluest of blue chips, so why has it fallen from the top spot among the Pros?  It’s impossible to know for sure, but in the aggregate, we can take a few guesses.

As the market turmoil hit hard in September, every stock with exposure to the financial sector fell under suspicion.  Thanks to its GE Capital business, GE was not immune to these concerns and some of the Pros may have decided to cut back their holdings.  JNJ, meanwhile, has held up remarkably well thanks to limited exposure to the financial sector and a portfolio of healthcare products that is regarded as recession proof.

Secondly, while GE’s loss of the top spot may have to do with the fact that quite a few Pros were trimming their exposure, the steep decline in GE’s share price during the quarter also contributed.  We only show Pros’ top-15 holdings on tickerspy, so if the price decline during Q3 caused GE to slip out of a Pro’s top-15 holdings, we count that as a “Pro Holder Remove.”  During Q3, JNJ fell by about -5% while GE stock dropped by about -27%.

The rest of the Pro favorites top five for Q3 is Exxon Mobile (XOM), Procter & Gamble (PG), and Microsoft (MSFT).

All the Pro portfolios for Q3 have been added to tickerspy. Click below to check out the latest holdings:

• Berkshire Hathaway
• Capital Growth Management
• Pabrai Funds
• Fairholme Capital Management
• Lone Pine Capital
• Tiger Global Management
• Carl Icahn
• Atticus Capital
• Third Avenue Management
• Greenlight Capital

You can find many more by digging into Pro lists in our Ideas & Research section.

From tickerspy’s inception until about a week ago, Apple (AAPL) had been the most tracked stock on the site.  But now GE (GE) has taken over the illustrious top spot.  Given the rough market this fall, the shift isn’t altogether surprising.  Even a brand as stellar as AAPL has come to be viewed as a risk thanks to its exposure to consumer spending.  Meanwhile, GE hasn’t exactly escaped the carnage.  The bluest of the blue chips is down about -45% in 2008, and the stock took a capital infusion from Warren Buffett in an effort to dampen concerns about its troubled financial unit.  Nonetheless, GE has benefited from being perceived as a safe haven, and its yield — now sitting around 6% — is looking attractive.