Will new version of Mono used in Unity 3.0 include IKVM.NET, or will it be cut out?

Just wondering.

Mono doesn't actually include IKVM - it's a separate project.

No way to tell. Everything about Unity 3.0 is classified and no information other that what has been shared so far, is hidden till the release. Some stuff will be answered with the pre-release for the people that buy it early. But even then, things are subject to change.