The question really depends on the type of site you are going to build, especialy on the complexity of the buisness logic and data (and the size of the data).
IMHO there are 3 major cases:
a) Small or Small->Medium
Interpreted language - Python using Django, PHP using Zend or Ruby using Rails.
Pro: This offers the best productivity, that is you can obtain a functional product very fast.
Con: The problem with this is the limited logic that can be applied on the data scalability and performance problems.
C# using .NET
Pro: Advantage in performance and security over the previous due to a compiled and typed language; also lots of advantages from Microsoft Visual Studio which automates very much, from deploying into cloud to object-relational mapping.
Con: Closed source, costs, Windows bounded;
c) Medium or Large - where middleware has a purpose of existence
Java using JSF, Struts or Spring MVC
Pro: Designed for scalability and platform independence; has many open source frameworks//APIs for many things (from Spring MVC as a web frameworks to Hadoop for distributed computing or JMS for middleware communication)
Con: Kind of complex
And now to argument my opinion why I believe Java is suitable for large applications while .NET is not. A large application is likely to be complex so it needs to be flexible and customizable; the technology for Java is mostly open source (and directly customizable) while most of the technology for .NET costs money and closed source. I also mentioned that .NET is good for the automizations that come with VS; but the problem with this automatizations is that it does not build flexible and elegant code. This kind of code is needed to be written by a real programmer; so the money paid for VS and other MS technologies are not worth to be paid for since the application is to be flexible and the code still needs to be written by real programmer. You can actually write complex applications using C#, it's just not profitable. And Java has also the advantage of platform independence.
Just a subjective opinion.
I sugest you choose something from the first category, since probably you are not speaking for a large enough organization so you have the money for Microsoft technology or for the manpower necesary for a complex Java application.