Hmm, it seems I have totally forgot to mention I got "Cross-Platform.NET Development" from Apress. It has a wealth of good advice for dealing with .NET, mono, and Portable.NET in a portable fashion. It covers very well the basic differences and probably more importantly the strategy and way to think about portability in the .NET world. Should be of particular use to Windows/.NET projects looking to migrate to more platforms and also Java people (who always seem very concerned with how portable something is) thinking about migrating and wondering if they will lose portability. If this sounds like you I would encourage you to check it out at http://cross-platform.net/. All this and I have only had time to go half way through it.
I also recently did some more work on monocop, and I think it is ready to be released to the public.