Rocketboom, the popular news and entertainment show which has pioneered a number of innovations for online video programs, has chosen Blip.tv as a publishing partner. Besides taking on the duties of serving new and archived videos, Blip.tv will also be helping the show sell advertising, and has introduced a new clickable, closable overlay bug for in-video ads. Beyond a slight change to media permalink URLs, the change should be completely transparent to Rocketboom viewers.

The move makes all sorts of business sense, as not only will Rocketboom realize increased revenue from this and other sponsorships, the company can also slash the cost of bandwidth completely from the budget. Blip.tv, which thanks to economies of scale, pays much less for bandwidth than Rocketboom does. “We’ll be taking over the bandwidth bill,” Blip.tv CEO Mike Hudack said and pointed out that Rocketboom as switched their Flash format to Blip.tv’s show player, which also features the ads.

The release coincides with a new sponsorship deal to promote the second season of Comedy Central’s The Sarah Silverman Program. Clicking on the lower-third overlay will bring viewers to a page on Comedy Central featuring video clips from Silverman and friends. The ad, enabled by Quicktime’s multimedia features, will only display to online viewers, even if downloaded via iTunes — though if viewed on Apple’s iPod, iPhone or Apple TV (where users can’t click), it won’t appear.

Blip.tv will be recouping costs through a share of any ad revenue they bring to Rocketboom, with deals brokered by Hudack and Dina Kaplan. The startup, which just secured a new, larger space for their office in downtown Manhattan, plans to bring on a full-time advertising sales representative in the near future. The deal with Viacom-owned Comedy Central was brokered with interactive agency Deep Focus, and Blip.tv will also be able to leverage relationships with advertising networks to move unused inventory.

With help from Apple’s Quicktime team and interactive advertising technology provider Aweli, the new Quicktime overlay ads provide not only Flash-like interactive functionality, but also advanced reporting statistics. The new system will work with any popular ad tracking service, and while eventually Blip.tv will be able to provide some data on ad viewing stats, for now it’s limited to tracking clicks.

It’s certainly a feather in Blip.tv’s cap to bring on what many consider the gold standard in online video shows. Rocketboom can now focus on creating the content rather than worrying about building a sales team. Ask A Ninja has a similar arrangement with Federated Media, which also sells ads for the GigaOM Network.