I want to make a backup copy of a fedora core 3 system. Just copy over the whole filesystem on an other HDD, so when the first one crashes I just have to write a boot loader on the backup an it would work like the old.

But I have no idea which dirs I should copy - and which not!
my guess is this:
Copy: bin boot etc home initrd lib misc opt root sbin selinux sys usr var

NOT copy: dev, lost+found, media, mnt, proc, tmp

But I'm not sure! Will dev and proc be regenerated by the kernel?
Would this copy work when I try to use it, in case I need this backup?

Why don't you just, temporarily, swap out the drives and do a minimal install on the other one?

because I'd prefer to just make a copy...