HD is dying, maybe? - how to save apps and system?

My HD clicks - but I really think it's clicked for the past 6 years since we got it.
Local store says it's time to replace HD, they heard it click over the phone. How do we transfer data easily to a new HD once we have one put in the tower? [I love my OS 9.1 and hope to continue using it, along with upgrading to Tiger and getting more memory and another HD added.]
I have copied [drag and drop] all the files onto a LaCie 500GB HD [formatted for OS 9 and X] to transfer them to the new MacBook Pro.
Should I also try to copy [draganddrop] all the applications in my application folder and the System Folder. Will these be useful when we try to get all the info back onto a new HD? [I don't know the technical term for what we need to do - sorry]
When I tried to copy the system folder yesterday, the screen froze with only 1 minute left to copy of a 5 minute copy event - the tech support help at the store bailed me out! [The day before I copied a photo folder that took 25 minutes to do without a hitch]
Now, I'm scared to even use the G4 to prevent it from dying before I can get a new HD - but I have a lot of work to do on it and not on the MBP. Is is possible it really has been clicking for years, and I shouldn't worry just yet - I have to get the current work I'm doing done before I give it up the G4 for repairs - and hopefully before it dies.
So - do I try risk copying the system folder and apps? [or is this irrelevant as one guy at the store said]
-do I stop using the G4 because it will be easier to put the system back together on a new HD it the old HD isn't dead?
-am I being hysterical and the HD isn't going to die in the next month - giving me time to finish this project???
Help please, and thanks in advance,
Mrs H

The Mac OS 9.1 Update can be found here. As for copying a pre-OS X hard drive, I start with the System folder first, followed by the Applications folder, then the Documents, Utilities, Apple Extras, and CD Extras folders. Because many programs install resources within the System folder, that one is essential to accurately copy without any glitches. If the hard drive has a mechanical or electronic issue that affects the ability of the heads to traverse the hard disk platter(s) and read data, you could experience data corruption. If that occurs, you'd need to reinstall the applications from their original installer programs. I really think you'd be better off taking the time to reinstall the OS and assorted programs, so that you begin with a clean slate. It will take more time, but is probably worth the extra effort. When you download a program installer, I'd recommend copying it to some type of removable media device, so that it's available for future use.

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