I couldn't find anything that can do that for multiple langauges and still be customized enough.
What I did use for a while was Line Counter (lc.exe). You can download it here. Its a nice command line tool and support C/C++ and C#.
I also saw a project in codeproject written in C# that counts C# lines which you can get its source, so this just might be a good basis to write something of your own and fully customize it. You can see the project here.
Hope this helps.