Those transfer programs almost never work correctly.
It's always better to do a clean install. With use, the system tends to collect a lot of unnecessary files. Trial versions that didn't uninstall completely, tools you used some time ago but which are now outdated etc.
A new OS installation is a good way to get rid of the junk.
When I switched from XP to Win 7, I installed the new Win on a new harddisk. That way I didn't have to wipe the original installation. I could access the software directories to get back my customized data (brush settings for Photoshop, hotkey settings for various apps etc.), just copied those files into the corresponding folders on Win 7. But you've got to do that manually, it's the safest way to get what you need.