Clicking noise on startup, followed by folder with flashing "?"

Here are my thoughts... Sounds like your Hard Drive is about to take a long nap.

1. Most important backup now! If of course you do not already have a backup.

2. Once you have a good backup, boot from OSX install DVD and run "Repair Disk Permissions" and "Repair Disk" from Disk Utilities. While you are in Disk Utilities check the drives S.M.A.R.T. status, it should read "verified".

3. You may want to go ahead and do a reset on the Macs' PRAM.

http://support.apple.com/kb/HT1379

Let us know what the results are.

Well if that's what motivates you!

But I would try some of the above fixes, this is not a certainty that the hard drive is going south for eternity but it is very possible that's why I stress tha backup part.

It is the noise! along with the question marked folder that leads me to believe that the drive may be trying to takes its last breath.

Alot of times it could be a simple as running the disk utilities that I mentioned. Other times it could be as easy as removing excesive data from the drive. For example you usually need 10% to 15% of the drive space free. So for example, if you have a 320Gb drive then you should keep 4 to 6Gb free if you have a 160Gb drive then you should keep 2 to 3Gb free.

If your drive does not meet the above standards then this could also be your problem, as I've seen drives make these noises when they are full and working hard to move the data around.

Let us know what you find...

I have the the same problem. I´ll try your recommendations too.

Hope it works.

Do you happen to have a bootable external backup. Maybe you know someone with a Macbook or MBP that you could use, and you could utilize Target Disk Mode.

No.
You need to replace your disk drive.
Find a local Apple Authorized Repair shop. See http://www.apple.com/buy/locator/service/
The cost should be about $100 for labor + $150 for the drive.

It's difficult for Disk Utilities to diagnose sector issues on a drive in which is it running from. It would be like trying to put put a band-aid in the center of your back by yourself, hard to do accurately. This is why it is best to run the Disk Repair function from the DVD, the dvd loads software into memory and does not need the hard drive to run, this way it can accurately diagnose it. You'll be able to accomplish the same task by using a different drive with OSX loaded to perform the Disk Repair on your drive just like the DVD would do for you.

I do not believe that it is a OSX issue but that does not mean that Snow Leopard will not fix the problem. If you'd like to verify that then backup all your data, and then do an erase and install, which will put a brand new system on your Mac. Then if the problem persist then it is definitely the drive.

I still believe that you have a drive that may be failing or you have it full.

My iMac started doing the same thing a week ago. Do backup immediatly but before you condemn the hard drive and start throwing parts at it check this out http://support.apple.com/kb/TS2570.

My problem looks like it might be related to my printer. The system log is recording this time out every few seconds "*Oct 24 04:55:36 Sapphire kernel[0]: USBF: 1028.264 AppleUSBEHCI[0x38ea000]::Found a transaction past the completion deadline on bus 253, timing out!*". When I disconnect the printer the time outs cease. I don't yet know if this is related to the intermittent startup problem.