You will have to re-install almost all applications from scratch. I say almost, because there's some that don't write stuff into the registry (e.g. standalone executables) and therefore do not need installation.
But even for those you re-install, many allow you to bring over your preferences from the Docs&Settings applications / local settings folders - for example, I always just copy the entire Mozilla directory from old to new (assuming it's the same version), and this has never failed to bring all bookmarks, browsing history, cookies etc. to the new PC.
Also for Office applications, you can at least copy over the templates, including Normal.dot.
It is still a PITA, though. I've just gone through it on two PCs at home, going from Win XP 32-bit to Win 7 64-bit.
SD