Not to be pedantic, but .NET is a framework with multiple languages targeting the common language runtime, not necessarily just C#. With that said, you can actually get a Perl.NET add-in for Visual Studio from ActiveState and build your web applications using ASP.NET (think drag and drop web forms). Then you can have your comfortable Windows environment, your comfortable perl code, and even leverage the .NET write-once-run-anywhere abilities (think Mono) if you ever did want to move over to a linux environment (there is a mod_mono).
While this doesn't really answer "What should I use?" it does make you aware that your intial negative reaction to .NET could be easily soothed over. Ideally, you want to use whatever it is that makes your job easier. And using Microsoft technologies on Microsoft platforms can ease development. Remember that you want to be doing development rather than fighting with learning a new platform.
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