Today they launched FairSearch.org, a homepage for lobbying against the search giant’s proposed $700 million acquisition of ITA Software, a Cambridge, Mass.-based maker of airline reservations software. Among those raising concerns are Expedia, Kayak and Sabre Holdings (Travelocity).

The main grievance is that Google is trying to corner the airline search market. One scenario has Google launching its own travel search offering for consumers, thus disintermediating ITA-dependent sites like Kayak and Hotwire (owned by Expedia). Another fear is that Google will raise the prices of ITA offerings, thus pricing out smaller sites (and significantly reducing margins for larger ones).

“Combining Google and ITA – the dominant providers of web search and flight search technology, respectively – raises some serious concerns for travelers and the online travel industry as a whole,” said Expedia (EXPE) CEO Dara Khosrowshahi in a prepared statement. “We support this coalition because we believe consumers deserve transparency, and that they – not search engines – should choose winners and losers in online travel.”

Google, of course, denies the doomsday speculation. It says that it wants ITA data, and that the subsequent search results would help drive traffic to both airline and third-party ticketing sites. (Note: the airlines have been largely silent from this debate, even though some major U.S. carriers use ITA.)

While all of this plays out in Justice Department hallways, it’s worth noting that the spat has produced a couple of very conflicted parties: Venture capital firms General Catalyst Partners and Sequoia Capital, which have investments in both ITA and Kayak.

General Catalyst participated in the first outside funding round for both companies, and partner Joel Cutler serves on both the ITA and Kayak boards of directors. Sequoia came aboard a bit later, with partner Mike Moritz sitting alongside Cutler on the Kayak board. (Sequoia does not have an ITA board seat, although may have certain observer rights.)

Do Cutler and Moritz hope that ITA prevails, because it’s certain pennies in their pockets? Or do they hope Kayak can scuttle the sale, given that Kayak has raised more VC funding (i.e., investors are more pot-committed) and some other exit could be devised for ITA (alternate sale or IPO)? And how are Kayak and ITA handling the matter at the board level?

Lots of questions, but no answers yet (not even canned, non-committal ones). I’ve left messages for General Catalyst and Kayak, and will update this post if I hear back. Moritz and ITA declined to comment.

Update: We just got a statement from Robert Birge, Kayak’s chief marketing officer. It doesn’t really answer how Cutler is handling the conflict, but here you go:

“KAYAK is an independent company with an obligation to do what is in its best interests. Mere common ownership interest by a VC is not a conflict. The two companies share only one common director, and to the extent that director has a conflict, he has an independent obligation to fulfill his fiduciary duties. He is one of 7 directors at KAYAK.”