While for the most part you can generate the same MSIL, there are definitely differences in tooling. PEX, for example, works much easier with C#.
What Microsoft or 3rd party tools don’t work equally well for both languages?
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I guess that answer depends on what you mean by tooling support.
For example, when it comes to IDE support, VB does a lot more than what C# does. It just has a better IDE.
It has extremely good background compilation and really good intellisence.
When it comes to support for MS research projects, or ‘new’ platforms like the XBox, VB will probably lag behind C#.
For things done by the MS Developer Division, or Office, you should expect more or less equal support between the two languages.
For other groups, like the MS research project you mentioned, multi language parity is often not a priority. In those cases they seem to tend to go with C# as their default choice.