Apparently you have to do this from the Visual Studio 2005 command prompt and not the Visual Studio 2008 prompt; it works now.
There really should be a better guide on how to enable Qt support for Windows Mobile ..

What is the problem with visual studio 2008?thanks for the help.

Why there is always a problem in Visual Studio 2008 prompt?thanks for help.

I managed to build Qt 4.7.3 for Windows Mobile 6.0 from the Visual Studio 2008 command prompt, using the wincewm60professional-msvc2008 mkspec, without any problems (except that I had to omit the examples, using the -nomake examples flag). So there is not “always a problem”…

I didn’t say there is “always a problem”; I had to do it from the VS2005 command prompt to get it to work. Using the VS2008 command prompt I could not get the configure.exe step to work, nor could I see any Qt/CE platforms in the QT4 Windows CE Project wizard.
Using the VS2005 prompt it all worked well; maybe because I’m running VS2005 Pro and only VS2008 Standard?

No, it was ‘leroy4perez’ who said “always a problem”. Anyway, it could be as you say. I only have VS2008 Professional installed, and it works just fine for me. Not sure what the “Qt4 Windows CE Project Wizard” is – something inside the Visual Studio IDE? I only use Qt Creator.