Debian or HDD or GRUB?
 

I unhooked my 2 HDDs and hooked up a different one with Windows on it (parents). I then took that off and hooked everything-data cables and power cords up how they were before. Now, Debian won't boot and Windoze will. On boot, Debian freezes at "waiting for root filesystem". Currently I'm downloading Knoppix again to recover my files, then I may install something else. I have found Debian very fast, but very touchy. I may switch to a slightly more stable distro.

I would however like to be able to boot Debian and copy files that way. Oh well...

Debian is one of the most stable distros out there. I suspect there's a problem with the way you hooked the cables up, or the bios reordered the drives. Also note the jumper positions on the drives.

But would the BIOS reordering the drives change how it Debian works though? It goes directly from GRUB to Debian how I set it up, but says its waiting for the root filesystem. I even tried unplugging my other hdd, and Debian still won't boot.

Yes, it would.

Assuming your drives are IDE, Linux will name them this way:
hda - BIOS primary master
hdb - BIOS primary slave
hdc - BIOS secondary master
hdd - BIOS secondary slave
hde through hdh - third and fourth IDE, if your motherboard supports that