I've read through this and countless other posts about this issue (which I am also experiencing).  It truly does render the computer useless.

The only big thing that jumps out at me in this thread is that everyone is mentioning problems with their CD/DVD drives, and upgrading firmware, etc.  So... I don't even HAVE an optical drive installed on the system, and this problem happens every time I boot.  

I do have an Intel chipset, and I was thinking I'd try blacklisting the ata piix module, but currently I am remote (over ssh), and the computer takes several minutes to respond even to shell commands.  So I'd venture to say this isn't only a problem with optical drives.  All I have is 3 internal SATA drives.  No external USB, no optical, no floppy.  I also tried stopping the HAL daemon, and initially it seemed  JUST A LITTLE better, although the messages still show up in the syslog.  I don't know if I should try to blacklist ata piix while I'm remote, as I've noticed in reading through posts that it might render the machine unbootable.

Anything else I can try? This is running Intrepid with all recent updates, 3 internal SATA drives, two of which are using mdadm for 3 RAID1 partitions and 1 RAID0 partition.  And I've done countless diagnostics and all hardware appears normal.  Also, I've removed the third (non-RAID) drive and the problem still happens.  errors:

Jan  5 10:10:15 kaya kernel: [ 6132.945046] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
Jan  5 10:10:15 kaya kernel: [ 6132.945062] ata3.00: cmd c8/00:08:61:36:db/00:00:00:00:00/e5 tag 0 dma 4096 in
Jan  5 10:10:15 kaya kernel: [ 6132.945066]          res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
Jan  5 10:10:15 kaya kernel: [ 6132.945074] ata3.00: status: { DRDY }
Jan  5 10:10:15 kaya kernel: [ 6132.945090] ata3: soft resetting link
Jan  5 10:10:15 kaya kernel: [ 6133.181465] ata3.00: configured for UDMA/100
Jan  5 10:10:15 kaya kernel: [ 6133.181487] ata3: EH complete
Jan  5 10:10:15 kaya kernel: [ 6133.194973] sd 2:0:0:0: [sda] 234441648 512-byte hardware sectors (120034 MB)
Jan  5 10:10:15 kaya kernel: [ 6133.195229] sd 2:0:0:0: [sda] Write Protect is off
Jan  5 10:10:15 kaya kernel: [ 6133.195236] sd 2:0:0:0: [sda] Mode Sense: 00 3a 00 00
Jan  5 10:10:15 kaya kernel: [ 6133.221708] sd 2:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
Jan  5 10:10:46 kaya kernel: [ 6163.908049] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
Jan  5 10:10:46 kaya kernel: [ 6163.908063] ata3.00: cmd c8/00:20:89:30:db/00:00:00:00:00/e5 tag 0 dma 16384 in
Jan  5 10:10:46 kaya kernel: [ 6163.908065]          res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
Jan  5 10:10:46 kaya kernel: [ 6163.908071] ata3.00: status: { DRDY }
Jan  5 10:10:46 kaya kernel: [ 6163.908083] ata3: soft resetting link
Jan  5 10:10:46 kaya kernel: [ 6164.144466] ata3.00: configured for UDMA/100
Jan  5 10:10:46 kaya kernel: [ 6164.144487] ata3: EH complete
Jan  5 10:10:46 kaya kernel: [ 6164.161017] sd 2:0:0:0: [sda] 234441648 512-byte hardware sectors (120034 MB)
Jan  5 10:10:46 kaya kernel: [ 6164.161303] sd 2:0:0:0: [sda] Write Protect is off
Jan  5 10:10:46 kaya kernel: [ 6164.161314] sd 2:0:0:0: [sda] Mode Sense: 00 3a 00 00
Jan  5 10:10:46 kaya kernel: [ 6164.175907] sd 2:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA