Miguel de Icaza posted On Fragmentation in response to a Linux open source developer.>  In it, Miguel hints at the path I believe Mono is going to take in the future.>  Essentially, he argues that applications should have a large “core” of code that works on all platforms, and then has platform-specific code to ensure the best performance and appearance on each supported operating system.

Java approaches the issue with making the entire code base cross-platform.>  But as Miguel points out, “[Y]ou always end up with an alien application: either the look, or the integration into the platform is substandard.”

On the opposite end of the spectrum, Microsoft promotes the all-MS platform, opening up only to standards-based transport protocols, such as SOAP, TCP/IP, etc.>  In response to wrapping Longhorn in order to stick to the Java approach, Miguel said, “No ISV will pick a layer on top of the Longhorn layer on Windows today or tomorrow: .NET is simple, easy to use as opposed to older APIs. ISVs will demand native support for them.”>  Amazing business sense for a techie; no wonder Don Box wants him to work for Microsoft.

Miguel’s conclusion is:

“The botttom line is: no technology today gives you transparent portability. The best bet today is to share as much as possible on your "engine" and redo the OS integration components for each OS you support.”

Thanks to Ken Brubaker for pointing out Miguel’s blog post here.