Apple has trademarked FaceTime: http://www.patentlyapple.com/patently-apple/2010/06/apple-wa...

IANAL, but Apple's trademark seems to cover software as well as mobile devices.

Meanwhile, Facebook is trying to trademark "face": http://techcrunch.com/2010/08/26/trademark-face/

So I think the answer is: "pick another name". The question I'd ask, is if you have no relation to Facebook or FaceTime in the application and have no expectation to receive goodwill based on those apps, why would you want to have a similar name?