I was running Super Duper to clone my Mac's internal drive to an external hard drive when it stopped and gave a red error message.

I ran Disk Utility's Repair Disk and got the message that the external drive had an invalid node structure (it made a noise that is reproducable). This external Firewire drive is my only backup. It is a Seagate in an OWC enclosure.

Any ideas on how to fix this drive? It rarely gets used except on monthly backups. (My Mac's internal drive checks out OK).

My best guess is that the drive has failed. Seagate has had a bad reputation for quite awhile. See if any of the sounds available here are similar.

I'm thinking about going with OWC. Can I boot from a OWC Mercury On The Go Firewire drive? I googled and it looks like there are problems. I know nothing about their reliability and would welcome any suggestions regarding buying an external drive I can boot from.

I've got 60 GB of my 120 GB imac internal drive used, so I don't need a big drive for backup. I use Super Duper to clone the internal drive.

You don't have to buy a whole setup; get a new drive and put it into the existing enclosure after removing the Seagate. FWIW, I have had good luck with Hitachi drives but Western Digital has a fine reputation also. OWC is a very reliable company so it would be worthwhile to phone them for advice. I have found their tech support to be excellent.

invalid node structure is one of those things that requires stronger tools like diskwarrior to fix. and I have yet to see diskutil succeed when it says it's 'rebuilding catalog b-tree".

Hopefully, you're right about Disk Warrior. The peculiar sounds from the drive seem to be ominous, however.

even if it can't fix it, it will probably be able to preview it for recovery. I use this frequently.

dw will say that it can't replace the directory because of a mechanical failure, instead of attempting to write to an already malfunctioning drive. Which is a good thing.

Well, for the price of Disk Warrior I can get a new drive.

If I were you, I would do both. Even if DW can repair the problem, the noises from the drive don't exactly inspire confidence. I have had DW for many years and it has gotten me out of a few jams. As far as I'm concerned, it is an indispensable part of my arsenal. Disk Utility is fine, mostly, but sometimes you need an industrial strength utility.

I settled on an OWC On the Go drive.

My only question now is, with Disk Utility, do I initialize the external FireWire drive as Apple Extended (journaled) or GUID, keeping in mind I have an Intel Mac.

You want GUID, which should also include Mac OS Extended (journaled).

GUID is the partition table type and is the preferred type for OS X. Mac OS Extended is the format and [u](Journaled) is an option that keeps track of changes to the file system and makes recovery quicker and easier. Journaling is also used by OS X to facilitate Spotlight and Time Machine. Your disk should have a GUID partition table and be formatted Mac OS Extended (Journaled).