Failure of internal drives? Reliability concern....

I've just moved to a new Mac Pro after a catastrophic drive failure of my old one. The old one had the Apple OEM 250G internal drive and a WD 750G additional internal drive. The WD drive had 2 partitions, both of them Carbon Copy Cloner clones of the main drive. (One clone was an exact mirror, one clone was an incremental backup clone.) Both partitions were bootable clones, and I had booted from both in the past without any problems.
Both internal drives died at the same time. Disk Utility couldn't repair them. DriveWarrior couldn't repair them. I couldn't access either drive via Target Disk Mode or in safe mode or in single user mode -- I couldn't even open a directory window on either drive without getting a permanent spinning beach ball that required a hard power-off. I removed the drive with the clones, and took the machine in to the Apple Store with just the original drive in place. They told me it was a bad drive. The other drive was displaying the same symptoms, and I'm assuming that it's bad too.
So.... BOTH drives failed, pretty much at the same time. I find it hard to believe that two drives failed simultaneously on their own. I tend to think it must have been some "original cause" that killed both, although I have no idea what that cause might be.
I'm now in search of a reliable "bootable clone" backup system. I'm not worried about my user data. Retrospect runs every night and backs up my entire user directory to DVDs, and that saved my bacon so that I didn't lose everything. Retrospect restored all my data files from my user directory within a few hours. I also have cron scripts that run that backup my MySQL databases every night.
But..... losing my main drive and my clones was almost as bad as losing my data. I had a custom apache file with tons of virtual hosts, the Entropy php packages, PEAR and PEAR packages, ImageMagick, mysql, various unix utilities and CPAN modules.... In short, a highly customized system that is not easily re-creatable when you're starting from a fresh system install. Several days after bringing the new Mac Pro home, I'm almost back to where I was.
I had always thought that having not one but two bootable clones would protect me against this situation. It turned out I was wrong.
I've already decided that my two clones will never again be separate partitions on the same drive, since a drive failure means both clones are gone. And I'll have at least 3 clones, on 3 separate drives -- two mirrors along with the incremental backup.
Is there any risk in having my bootable clones as internal drives? Could something in the old computer have caused the drive failures? The ease of installing additional internal drives seduced me into using an internal drive, and now I wonder if that was a mistake. Would I be better off cloning to external FW drives? In the past, I had always cloned to external drives, and I've never had one fail. I'm wondering if I should invest in multiple external FW drives, rather than internal SATA drives.
Can anyone provide any insight as to why two internal drives would fail at the same time? This is the part that has me most concerned, and it's why I bought a new machine, rather than simply replacing the drive in the old one. I don't think I could ever fully trust the old machine again, because it seems like there had to be something going on to cause simultaneous drive failure.
Is SuperDuper more reliable than Carbon Copy Cloner for making bootable clones? I've never had problems with CCC in the past..... but while I'm re-evaluating my backup strategy it seems worth looking into.
Is it worth it to boot from another volume in order to have CCC or SD do a block-level clone, rather than a file-level clone? I haven't usually done that in the past, but if will save me from another week in ****, I'll spend that extra few minutes on a regular basis.
Is there any other cloning system that's more reliable than CCC or SD?
What can I do to protect against multiple simultaneous drive failure?
Bottom line: What's most important to me is a bootable clone of my entire system. I can spend the money for the most appropriate internal or external drives.

TDM is firmware, so it's tied to the motherboard. But if the old machine tested out OK but the drives still are dead, then I guess it was simultaneous failure even though that would be rare, statistically.
I do not use my mirrored RAID except as the backup for my system drive. A mirrored RAID is made up of two identical drives (not necessary but less likely to have problems if the drives are identical) in which one drive acts as a mirror of the other. The RAID configuration automatically writes to the second drive in the RAID anything that's written to the first drive in the RAID. See the following for more info on RAIDs:
RAID Basics
For basic definitions and discussion of what a RAID is and the different types of RAIDs see RAIDs. Additional discussions plus advantages and disadvantages of RAIDs and different RAID arrays see:
RAID Tutorial;
RAID Array and Server: Hardware and Service Comparison>.
Hardware or Software RAID?
RAID Hardware Vs RAID Software - What is your best option?
RAID is a method of combining multiple disk drives into a single entity in order to improve the overall performance and reliability of your system. The different options for combining the disks are referred to as RAID levels. There are several different levels of RAID available depending on the needs of your system. One of the options available to you is whether you should use a Hardware RAID solution or a Software RAID solution.
RAID Hardware is always a disk controller to which you can cable up the disk drives. RAID Software is a set of kernel modules coupled together with management utilities that implement RAID in Software and require no additional hardware.
Pros and cons
Software RAID is more flexible than Hardware RAID. Software RAID is also considerably less expensive. On the other hand, a Software RAID system requires more CPU cycles and power to run well than a comparable Hardware RAID System. Also, because Software RAID operates on a partition by partition basis where a number of individual disk partitions are grouped together as opposed to Hardware RAID systems which generally group together entire disk drives, Software RAID tends be slightly more complicated to run. This is because it has more available configurations and options. An added benefit to the slightly more expensive Hardware RAID solution is that many Hardware RAID systems incorporate features that are specialized for optimizing the performance of your system.
For more detailed information on the differences between Software RAID and Hardware RAID you may want to read: Hardware RAID vs. Software RAID: Which Implementation is Best for my Application?

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