It's really not the version of Xcode that's relevant. It's the version of the SDK that the project was built against. The latest version of Xcode is 3.1.4 in the 3.1beta SDK, at least that's the latest version I have.
I'm pretty sure that Apple will accept apps compiled against any SDK between 2.0 and 3.0, inclusive. 3.1 is still in beta.