In deals the size of the one that Microsoft just agreed to in acquiring Skype for $8.5 billion, there are always interesting little wrinkles that come out of the woodwork after the announcements are made and people have a chance to dig deep.

The “good” of this deal is that as part of the Skype package Microsoft now also owns Qik, the streaming mobile company that Skype acquired for $121 million earlier this year. Any details beyond the fact that Qik was indeed part of the whole package are pretty sparse.

The ironic thing about the deal is that, as Todd Bishop from GeekWire pointed out, is the platform coverage that both Skype and Qik has – neither included Windows Phone.

From a mobile perspective, the overall Microsoft and Skype deal is somewhat ironic. Skype has apps for iPhone and Android but not for Microsoft’s Windows Phone 7. Qik has apps for Android and iPhone, and Windows Mobile, Microsoft’s older mobile operating system, but it doesn’t offer a Windows Phone 7 app.

On the “bad” side of the deal, Jared Newman at Technologizer writes that the subscription music startup Rdio could be in trouble due to a $6 million investment that Skype had in the company.

Skype has a $6 million investment in Rdio, thanks to some lawsuit madness involving Skype’s founders and several Silicon Valley players. Kafka said he’s “pretty sure” Skype and Rdio were planning to deepen ties and drum up more users for the music service.

But Microsoft has its own music service, Zune Pass, and it seems unlikely that the company will want to manage a competitor. For now, neither Microsoft nor Rdio are commenting.

In Jared view Rdio has to options: approach Microsoft for a merger/acquisition, or close its doors. Personally I think that there are a couple of other options, those being: Find an investor to buy Skype’s (now Microsoft’s) share or just carry on business as usual and hope Microsoft doesn’t come knocking.

[Cross-posted at Winextra]