Another possibility is if the OCZ Agility drive has been mounted with the "discard" flag set (look in /proc/mounts for "discard").
Not set.
I'm using Linux Mint 17, if that makes a difference.
Eg. "hdparm -J30 /dev/sdX". The settings change need only be done once, and is permanent unless modified again.
Done. I'm not convinced that this was the problem: my "working set" of data is on the SSD -- the WD drives are only used for big stuff: downloads, games, movies, music, etc.
Also, it just hiccuped again while typing this: immediately after I made the change.
Oh, and because this behaviour only just started happening. I've had the PC for about 2 years now.
I haven't rebooted into the new kernel yet, though.
Some more information: the PC itself doesn't seem to hang. That is: no process seems to be affected. Keystrokes aren't dropped, as far as I can tell; they just seem to be delayed. Well, either they're delayed, or the video output corresponding to the keystrokes is delayed.
Oh, the graphics card:
$ lspci | grep VGA
03:00.0 VGA compatible controller: NVIDIA Corporation GK104 [GeForce GTX 760] (rev a1)
$ cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 331.113 Mon Dec 1 21:08:13 PST 2014
GCC version: gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)