With the obvious differences that come with using two different OSes, there are some that are a bit more subtle - like the values in PHP of $_SERVER between IIS and Apache. John Cox tackles this in this latest post on his blog.

I think one of the most frustrating things about web development is designing applications for multiple platforms. Whether my frustrations lie with developing applications for multiple PHP versions with multiple cache systems or designing CSS for multiple browsers, nothing is more frustrating than having applications work on multiple server software. That is why I absolutely love every cheat sheet that I can run across for these situations.

This cheatsheet lists just about every $_SERVER value I can think of and where its supported (between Apache, Apache SSL, IIS, and IIS SSL). They've also marked the ones in bold that are availible consistently across all of the setups...