There are a number of interfacing projects on the web that deal with parallel ATA or IDE hard drives. Many of them use the old 8255 triple 8-bit I/O port chip, so something must be possible with the AVR/Arduino. Have a look at his one:
http://www.pjrc.com/tech/8051/ide/wesley.html
This example is beased on the ZX Spectrum:
This is generically Z80 based:
http://www.retroleum.co.uk/ide_interface.html
And this is the page on disk drives from the PIClist site: