Affiliate network KowaBunga! Marketing was acquired Monday for an undisclosed amount by CGI Holding Corp. It looks like Todd Farmer, who founded KowaBunga and is currently CEO of the company, will continue to head up the subsidiary following the merger.

KowaBunga, which started in 1996, now has more than 2,000 merchants using its My Affiliate Program Tracking and Management solution. In addition, thousands of affiliates are part of KowaBunga’s newly released Kolimbo Affiliate Network.

What seems unclear is how exactly how this deal fits in with CGI’s recent acquisition spree. Earlier this month CGI signed a letter of intent to buy a New Jersey affiliate marketing company called PrimaryAds in a deal that is estimated to be worth as much as $26 million.

CGI Holding, which is seeking shareholder approval to change its name to Think Partnership Inc., also recently entered into an agreement to merge with privately-held Meandaur, which does search marketing under the name Proceed Interactive.

CGI currently has seven subsidiaries: WebSourced, a search engine optimization and pay-per-click campaign management company; MarketSmart Advertising, Rightstuff, which does business under the name Bright Idea Studios) and Checkup Marketing, which all provide off-line advertising, public relations, marketing, branding and shopping evaluation services; Cherish, an online dating company; Ozona Online Network, which provides a full range of Web design, hosting and e-commerce solutions; and KowaBunga.

I haven’t heard much from KowaBunga affiliates on this one. I’d like to know what you think.