STAY AWAY FROM AUTO* and configure. These are horrible IMHO.
If you can somehow get a VS 8 or 9 vcproj/sln, you can use this. I have not used it, so I can't give any advice.
If you're up to manual conversion, I would suggest something like CMake, as it's pretty easy to get ready fast enough, even for large projects.
If the project has a simple layout, you could have success using Qt 4's qmake like this:
qmake -project
It will output a qmake .pro file, which can be converted into a makefile on many platforms (using qmake). This should work okay, but not perfectly. Alternatively, you can install the Qt plugin for VS, and let it generate the pro file from an existing VS project. It will make your build system depend on Qt4's qmake, which is probably not what you want.
There are of course other things like cmake, but they will all require manual intervention.