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Let me see... Several years ago I did a rm * in / on an AIX box. I recovered by copying the missing files from a similar machine.
The biggest one that I regret was a mistake I made when trying to change a partition from Linux ext2 to ReiserFS. My machine was dual bootable between W2k and RedHat. I had fdisk'ed and forgot to reboot before formatting the partition. I ended up wiping the NTFS partition that contained tons of original digital photographs, some of my daughter right after she was born. I would have rather lost my machine than those pictures.
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