That depends on your requirements. If you want to build everything in .Net or if you have single signon requirements on an intranet with everyone using internet explorer, it's a pretty easy choice.
You don't have to deploy ASP.NET projects to Windows boxes. You can use Apache/Nginx/whatever, Mono, and MySQL (or probably PostgreSQL, though I've not tried this) to replace IIS, .NET Framework, and SQL Server. There are a few differences here and there and it's not likely going to be as easy as deploying to Microsoft's webserver stack, but the savings on a farm of Linux servers vs. a farm of Windows servers (or even of a Linux VPS vs. a Windows VPS) should make it worthwhile if you're already up to speed on C# (or your language of choice), ASP.NET, etc.