Compatibility with IIS and Apache -- PHP, Python, etc?
Your lowest common denominator for building apps to seemlessly run on both the LAMP and Microsoft stacks is PHP.
Perl is another option, it's well supported on both Windows and Linux/Apache. But I think I'd be choosing PHP over Perl because of support for FastCGI which improves reliability and performance on the Windows stack. Microsoft and Zend have been doing a lot of work on PHP for Windows so that you can write PHP apps and confidently expect them to run well on both platforms. The proof of the pudding of this is that Joomla, WordPress, phpBBS and many other of the well known open source PHP applications run straight out of the box on Windows. 
Also as a developer and third line support engineer for a shared web hosting company, with a fair bit of experience in this area, I'd say that PHP on Windows is every bit as flexible, performant and reliable as PHP on the LAMP stack.
Finally, Ruby on Rails and Python/DJango aren't well supported options on IIS and will be non-existant on shared hosting platforms. This is mostly due to the amount of console access you'd need to knock things into shape to be able to run Rails/DJango.
I'm currently planning out a web app that I want to host for people and allow them to host themselves on either Linux/Apache of IIS6 or IIS7 (for the benefits of bandwidth, directory services [login, etc.]). 
I see that PHP is supported on both platforms. I've heard people serving Django and Python in IIS using PyISAPIe. I'm not sure about Ruby/Rails on IIS until IronRuby ships. I don't have much Perl experience but understand it would run in IIS as well.
Anyone have input for me? Thanks in advance.