It turns out that x64 support, whilst not explicitly stated, just works. If you set your environment up to use the x64 tools by running \Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\amd64\vcvarsamd64.bat
then run configure.bat for your compiler and build as normal you end up with appropriate libs and dlls.
Unfortunately the x64 libs build to the same names as the x86 libs so it's not possible to have a 'side by side' installation of STLPort to allow you to build with either x86 or x64.
Edit: I've written up what you need to do to provide side-by-side x64 and x86 support as well as packaging up the changes required for vs2008 builds on my blog. See here: http://www.lenholgate.com/archives/000812.html