Although Atlassian's applications are written in Java, you should have no issues using them in a .NET shop. The only concern that comes to mind is, should you ever want to write plug-ins, they would need to be written in Java. However, if you are using the hosted version (i.e. JIRA Studio) this may not be a consideration.
Tools like FishEye and Crucible will integrate with several popular source control systems (Subversion, Git, Perforce, Clearcase), so it just depends on whether your employer is using one of those systems or something else (Team Foundation Server, Visual SourceSafe, etc.) One thing to check if whether using the hosted version requires you to use their hosted install of Subversion as well. If so, it becomes more of an "all or nothing" decision.
In my case, we bought local install versions of all the Atlassian products and were able to use them seamlessly across Java, .NET, and Python development. For what it's worth, our team loved these tools and felt they were well worth the cost in terms of gained productivity.