The questions persist about this summer’s Yahoo! cliffhanger. What will the distant also-ran search engine do to boost both its search share and its earnings price? Will co-founder Jerry Yang be able to re-energize the company and stop the brain drain? Will Microsoft circle back for Buyout Offer: The Return? And whether or not any of those things happen, what difference will it all make for marketers?

The first group of questions is still open, but some industry experts have weighed in with educated, data-based opinion on a specific issue: namely, the search ad deal between Yahoo! and Google that has come to be known as “Yahoogle”.

This is the pact Yahoo! announced in mid-June—at the peak of the uncertainty about a possible unfriendly bid by Microsoft—that said in some instances, Yahoo! would serve up pay-per-click (PPC) search ads from Google rather than its own ads. The rationale was that the Google ads sometimes command higher prices per click than ads for the same keywords on the Yahoo! search marketing platform. That would bring in more revenue per search for Yahoo! (about $800 million annually, per the company), pleasing shareholders and Wall Street analysts, and staving off buyout offers.

The deal is still very vague. For one thing, it’s not certain how often or under what circumstances Yahoo! will opt to run a Google-sold search ad rather than one it has sold itself. And those specifics matter: If online marketers decided Yahoo! is going too often to the Google pile in placing PPC ads, those who now do search marketing on both engines may decide to save themselves some time (if not money) and concentrate on their Google campaigns.

Then too, federal regulators still have to agree that the ad deal between the largest search engine and the second largest does not constitute a monopoly. While no date has been set for any antitrust investigations, a Senate antitrust subcommittee heard testimony on the deal in mid-July. Chairman Sen. Herb Kohl kicked off the meeting by fretting that the ad arrangement could “reduce Yahoo! to nothing more than the latest satellite in Google’s orbit”, and that the two would then effectively control 90% of the search ad market.

Microsoft’s testimony didn’t allude to Google’s tractor beam capabilities, but it did argue that letting Google and Yahoo! cooperate in this way would effectively set a floor on search ad prices, which are usually set through a competitive auction. That would result in higher aggregate ad rates for search marketers.

Whether or not Microsoft is right about the overall anti-competitive aspects of the deal—and let’s face it, who knows more about stomping the competition?–research published last month by search marketing firm SearchIgnite suggests that in fact, search marketers may indeed pay more for certain types of keywords under this Yahoo!-Google arrangement.

The agency took a close look at 15,000 of the 20 million active keywords it managed for its clients from January 2008 through June. More specifically, it looked for keywords that ran not only on both the Yahoo! and Google platform but delivered PPC ads in the same position on the right side of the results page, since marketers often bid more to be the top ad on that right rail. SearchIgnite then took a look at the cost per click for the same keyword in the same rank on the two search engines, in an effort to see what impact letting Yahoo! serve Google ads might have.

SearchIgnite also sorted those 15,000 keywords into the buckets that search marketers commonly use: brand terms that include their trademarks or specific product names, head terms (commonly searched keywords), and tail terms.

That last group is those infrequent search words or phrases that often make up the majority of search marketers’ keyword lists. To some, they really are the heart of search marketing, because they let advertisers target relevant PPC ads to searchers looking for something very specific, and therefore they tend to convert better.

According to SearchIgnite’s findings, it’s exactly in those tail terms that the Yahoo-Google deal might produce the best revenue for Yahoo!, and the highest cost increases for search marketers. SearchIgnite’s research found that in almost all cases, tail terms on Google cost more for the same PPC rank than they do under Yahoo!’s current search ad platform.

The agency found that the same tail terms cost on average about 12% more in the first position on Google than they do on Yahoo! That price differential grows larger as the PPC moves down in rank, showing a 20% increase over Yahoo! prices in the third position and a 35% gap by the fifth rank. (Many search marketers won’t go past position five, since that commonly puts their ads below the fold.)

Yahoo! has already suggested that this ad deal will mostly kick in on these infrequently-search tail terms rather than the other categories. If that’s true, and depending on how thoroughly Yahoo! optimizes ad delivery to pick the most profitable PPC ad for each tail position, whether from its own ad bank or Google’s, then SearchIgnite concludes that the cost of running search ads on Yahoo! could increase by an average 22%.

“We always assumed at SearchIgnite that there would be a pricing impact for our customers [from the Yahoo!-Google deal],” says CEO Roger Barnette. “After all, Yahoo!’s not adding to their inventory with this deal; they’re just adding more marketers who will be bidding on that inventory.”

Barnette says his agency also assumed that the primary impact would be due to price differentials in tail terms rather than the more specific brand or head keywords. “Google just makes it easier to bid on large keyword sets,” he says. “Combined with the fact that they have more advertisers who spread out over a long tail, it made sense that the most significant price effects would come in those long-tail terms.”

In fact, SearchIgnite’s research found that when it came to prices for the same brand or head term in the same ad rank, Yahoo! often earned more per click than Google. A marketer looking to win the top slot for a PPC ad on a brand name, for example, paid on average 38% more on Yahoo! during the first half of this year, and 8% more for position number three. A head term (for example “SUV”) cost 16% more for the first and second ranks on Yahoo!

In other words, don’t look for Yahoo! to substitute Google ads in those ranks in the brand or head categories. The engine might deliver a Google PPC ad in the second, fourth or fifth brand slot, however; those all cost more on Google.

Barnette says assessing the true impact of the ad deal will have to wait on a clearer picture of how Yahoo! puts it into action—something that may come as soon as September, which the engine pointed to as the earliest start date for serving up Google search ads.

While anything that raises the floor bids for search ads will affect all search marketers, Barnette points out that clients using search agencies like his do so precisely to outsource the burden of finding the cheapest prices for keywords. The real impact, he says, may come among the smaller search marketers who are trying to manage their own efforts in-house and whose resources may already be stretched by trying to run two parallel online ad programs on Google and on Yahoo!

That may win Yahoo! some quick and dirty revenue increases, but Barnette points out that the deal may also eat into the search engine’s mindshare among marketers, who may come to see it as nothing more than that Google satellite Sen. Kohl referred to.

“Yahoo! is making a decision that will benefit their revenue in the short term,” Barnette says. “They’ll service their existing clients in their own bid landscape as they always have, but now they’re going to be able to pick and choose from another platform if those ad costs happen to be higher.

“But I think there’s a real concern that small and mid-sized businesses may decide it’s not worthwhile to manage multiple platforms any more, even if Yahoo!’s prices are a little cheaper. It might just be easier for them to bid directly on Google. So while Yahoo! would still be getting revenue from those customers through Google, they risk losing direct client contact with them. That may cost them the ability to upsell other ad products such as display ads that they’ve invested in heavily in the last few years.”