I've witnessed the same as Fugi, but to be honest that just doesn't feel right. What's worse than the feeling is that the old disk will statistically fail someday which will leave a ton of orphaned data behind. If at all possible just reinstall everything from scratch, possibly reducing the total amount of programs installed. That will clean up your Appdata folder as well, making the system run smoother.
Transferring settings and other user data for your applications from the old disk to the new one is of course essential, especially the AH settings.
There's programs that can transfer even programs from an old system to a new one, but the results vary. If they were fool proof, they'd be commonly used by everyone.