I've been able to use the standard Python modules from IronPython, but I haven't gotten SciPy to work yet. Has anyone been able to use SciPy from IronPython? What did you have to do to make it work?
Update: See Numerical computing in IronPython with Ironclad
Update: Microsoft is partnering with Enthought to make SciPy for .NET.
Anything with components written in C (for example NumPy, which is a component of SciPy) will not work on IronPython as the external language interface works differently. Any C language component will probably not work unless it has been explicitly ported to work with IronPython.
You might have to dig into the individual modules and check to see which ones work or are pure python and find out which if any of the C-based ones have been ported yet.
Some of my workmates are working on Ironclad, a project that will make extension modules for CPython work in IronPython. It's still in development, but parts of numpy, scipy and some other modules already work. You should try it out to see whether the parts of scipy you need are supported.
It's an open-source project, so if you're interested you could even help. In any case, some feedback about what you're trying to do and what parts we should look at next is helpful too.