This only applies to people using an Apple Extended Keyboard with a Mac, via an iMate or similar ADB-to-USB adapter. I hope it's useful to at least one other person.
The AEK's caps lock key is a locking ALPS switch, which means if you want to remap it to Command/Control, you have some work to do. Follow these instructions:
1. First, you need to physically exchange the locking switch with a non-locking switch. I swapped with Num Lock; you can also do something like Pause that you'll never use. I believe due to hardware constraints, this swap will render the donor key useless, so pick something you won't ever use. When you've decided, pop off the Caps Lock keycap and the target key's keycap. Take out the ALPS sliders using screwdrivers as prying tools (documented elsewhere) and exchange the assemblies. No soldering required.
2. Now, your Caps Lock will press like a normal key. But on every press, it will send both keydown and keyup codes due to the AEK's hardware. Gotta fix this.
3. Install KeyRemap4MacBook and PCKeyboardHack. Create a new profile for your AEK.
4. In PCKeyboardHack, check "Change Caps Lock" and change it to keycode 110.
5. In KeyRemap, open your private.xml and insert the following code:
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<item>
<name>AEK I caps lock to command fix</name>
<identifier>private.aekcapslock_fix</identifier>
<block>
<autogen>__KeyToKey__ KeyCode::PC_APPLICATION, KeyCode::VK_LOCK_COMMAND_L</autogen>
<autogen>__KeyToKey__ KeyCode::ESCAPE, KeyCode::ESCAPE, KeyCode::VK_LOCK_ALL_FORCE_OFF</autogen>
</block>
</item>
6. Go to System Prefs --> Keyboards --> Modifier Keys --> ADB adapter --> set caps lock behavior to "no action."
At this point, everything should be working as you want it to.7. (Optional) In KeyRemap, go to the "Status Message" tab and uncheck status messages so you don't see the lock notification every time you hold caps lock.
8. (Optional) Return to the system key modifiers dialog and set caps lock to another key.
9. Add the following to your private.xml and enable it for any non-AEK keyboard. If you don't include this, you'll have problems using caps lock with other keyboards. (You can get around this if you use clean private.xml code in which you define vendors and devices for every hack; I don't, so this is the sloppy way to do it).
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<item>
<name>Non-AEK caps lock fix, need for all non-AEK boards</name>
<identifier>private.nonaekfix</identifier>
<autogen>__KeyToKey__ KeyCode::PC_APPLICATION, KeyCode::CAPSLOCK</autogen>
</item>