My system has started behaving strangely, intermittently locking up. I see messages like the following in syslog:

Nov 18 22:22:00 claypool kernel: [ 3428.078156] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0
Nov 18 22:22:00 claypool kernel: [ 3428.078163] ata3.00: irq_stat 0x40000000
Nov 18 22:22:00 claypool kernel: [ 3428.078167] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00
Nov 18 22:22:00 claypool kernel: [ 3428.078182] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 22:22:00 claypool kernel: [ 3428.078184]          res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error)
Nov 18 22:22:00 claypool kernel: [ 3428.078188] ata3.00: status: { DRDY }
Nov 18 22:22:00 claypool kernel: [ 3428.080887] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0
Nov 18 22:22:00 claypool kernel: [ 3428.080890] ata3.00: irq_stat 0x40000000
Nov 18 22:22:00 claypool kernel: [ 3428.080893] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00
Nov 18 22:22:00 claypool kernel: [ 3428.080905] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 22:22:00 claypool kernel: [ 3428.080906]          res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error)
Nov 18 22:22:00 claypool kernel: [ 3428.080910] ata3.00: status: { DRDY }

And then this:

Nov 18 23:13:56 claypool kernel: [ 6544.000798] ata1.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
Nov 18 23:13:56 claypool kernel: [ 6544.000804] ata1.00: failed command: FLUSH CACHE EXT
Nov 18 23:13:56 claypool kernel: [ 6544.000814] ata1.00: cmd ea/00:00:00:00:00/00:00:00:00:00/a0 tag 0
Nov 18 23:13:56 claypool kernel: [ 6544.000815]          res 40/00:00:00:4f:c2/00:00:00:00:00/40 Emask 0x4 (timeout)
Nov 18 23:13:56 claypool kernel: [ 6544.000819] ata1.00: status: { DRDY }
Nov 18 23:13:56 claypool kernel: [ 6544.000825] ata1: hard resetting link
Nov 18 23:14:01 claypool kernel: [ 6549.360324] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:06 claypool kernel: [ 6554.008091] ata1: COMRESET failed (errno=-16)
Nov 18 23:14:06 claypool kernel: [ 6554.008103] ata1: hard resetting link
Nov 18 23:14:11 claypool kernel: [ 6559.372246] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:16 claypool kernel: [ 6564.020228] ata1: COMRESET failed (errno=-16)
Nov 18 23:14:16 claypool kernel: [ 6564.020235] ata1: hard resetting link
Nov 18 23:14:21 claypool kernel: [ 6569.380109] ata1: link is slow to respond, please be patient (ready=0)
Nov 18 23:14:31 claypool kernel: [ 6579.460243] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
Nov 18 23:14:31 claypool kernel: [ 6579.486595] ata1.00: configured for UDMA/133
Nov 18 23:14:31 claypool kernel: [ 6579.486601] ata1.00: retrying FLUSH 0xea Emask 0x4
Nov 18 23:14:31 claypool kernel: [ 6579.486939] ata1.00: device reported invalid CHS sector 0
Nov 18 23:14:31 claypool kernel: [ 6579.486952] ata1: EH complete
Nov 18 23:17:01 claypool CRON[3910]: (root) CMD (   cd / && run-parts --report /etc/cron.hourly)
Nov 18 23:17:01 claypool CRON[3908]: (CRON) error (grandchild #3910 failed with exit status 1)
Nov 18 23:17:01 claypool postfix/sendmail[3925]: fatal: open /etc/postfix/main.cf: No such file or directory
Nov 18 23:17:01 claypool CRON[3908]: (root) MAIL (mailed 1 byte of output; but got status 0x004b, #012)
Nov 18 23:39:01 claypool CRON[4200]: (root) CMD (  [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -print0 | xargs -n 200 -r -0 rm)

There are no messages marked after 23:39. When I next tried to use the machine, it would not return from the screensaver (blank screen), nor switch to another terminal, and I had to hard reboot it.

[UPDATE] The output of smartctl is here. I had trouble getting this, because / is being mounted read-only (?!), which prevents most applications from running.

Also, it may not be related, but I have the following worrying messages in dmesg:

[   10.084596] k8temp 0000:00:18.3: Temperature readouts might be wrong - check erratum #141
[   10.098477] i2c i2c-0: nForce2 SMBus adapter at 0x600
[   10.098483] ACPI: resource nForce2_smbus [io  0x0700-0x073f] conflicts with ACPI region SM00 [??? 0x00000700-0x0000073f flags 0x30]
[   10.098486] ACPI: This conflict may cause random problems and system instability
[   10.098487] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver
[   10.098509] i2c i2c-1: nForce2 SMBus adapter at 0x700
[   10.112570] Linux agpgart interface v0.103
[   10.155329] atk: Resources not safely usable due to acpi_enforce_resources kernel parameter
[   10.161506] it87: Found IT8712F chip at 0x290, revision 8
[   10.161517] it87: VID is disabled (pins used for GPIO)
[   10.161527] it87: in3 is VCC (+5V)
[   10.161528] it87: in7 is VCCH (+5V Stand-By)
[   10.161560] ACPI: resource it87 [io  0x0295-0x0296] conflicts with ACPI region ECRE [??? 0x00000290-0x000002af flags 0x45]
[   10.161562] ACPI: This conflict may cause random problems and system instability
[   10.161564] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver

[UPDATE 2] I swapped in a new SATA cable, per Phil's suggestion. The current output of smartctl is here, if it helps.

[UPDATE 3] I don't think the cable fixed it. The system hasn't locked up yet, but my media player crashed a few minutes ago and I have the following in the syslog:

Nov 20 16:07:17 claypool kernel: [ 2294.400033] ata1: link is slow to respond, please be patient (ready=0)
Nov 20 16:07:47 claypool kernel: [ 2324.084581] ata1: COMRESET failed (errno=-16)
Nov 20 16:07:47 claypool kernel: [ 2324.084588] ata1: limiting SATA link speed to 1.5 Gbps
Nov 20 16:07:47 claypool kernel: [ 2324.084592] ata1: hard resetting link

I get the following response from smartctl:

$ sudo smartctl -a /dev/sda
[sudo] password for chris: 
sudo: Can't open /var/lib/sudo/chris/0: Read-only file system
smartctl 5.40 2010-03-16 r3077 [i686-pc-linux-gnu] (local build)
Copyright (C) 2002-10 by Bruce Allen, http://smartmontools.sourceforge.net

Device: /0:0:0:0  Version: 
scsiModePageOffset: response length too short, resp_len=47 offset=50 bd_len=46
>> Terminate command early due to bad response to IEC mode page
A mandatory SMART command failed: exiting. To continue, add one or more '-T permissive' options.