unhook old HD so it's safe. Plug in new HD, install OS from scratch.
Now, hook up the new HD so that you have both up at the same time (the only reason to unplug is to keep any complications from happening and wiping your HD).
The only folders you'll need are /Applications and your user folder. Drag them over and replace the current ones, you'll probably need to authenticate and that should be it
IMHO you might want to copy over the /Library folder as well, since stuff like photoshop uses that.