I'm curious about how .NET will affect Python and Ruby applications. 
Will applications written in IronPython/IronRuby be so specific to the .NET environment, that they will essentially become platform specific? 
If they don't use any of the .NET features, then what is the advantage of IronPython/IronRuby over their non .NET counterparts?
You answer your first question with the second one, if you don't use anything from .Net only the original libs provided by the implementation of the language, you could interpret your *.py or *.rb file with another implementation and it should work.
The advantage would be if your a .Net shop you usually take care of having the right framework installed on client machine etc... well if you want python or ruby code, you now need to support another "framework" need to distribute install, take care of version problem etc... So there 2 advantages, using .Net framework power inside another language + keep the distribution/maintenance as simple as possible.
How will Python and Ruby applications be affected by .NET?