I prefer to keep programs on a seperate partition since the Windows partition fragments a lot

I also wouldn't give Windows a partition larger than 8 GB - though that might change with Vista, should I ever use it
I'd suggest you uninstall and reinstall the programs to the other partition, you'll save yourself a huge amount of headache otherwise from having to trawl the registry and change wherever else it might reference itself if it's not that tidy to keep it's settings there, plus all shortcuts etc. manually
