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I think menu.lst is what GRUB typically uses. Some distros (Red Hat to name one) use a hacked version of GRUB that uses grub.conf or a menu.lst file that is a symbolic link to grub.conf. That's my understanding, in any case. Someone correct me if I'm wrong...
For my distro, GRUB definitely uses the menu.lst file. In fact, grub.conf doesn't even exist as far as I can tell.