Aside from the "Modifier Keys" System Preferences section, I don't think an application can override the behaviour of the caps lock key..
I'm fairly sure the Caps Lock key event is not passed to applications, nor can they override the toggle effect.. Maybe you could do something whereby you monitor caps lock key state, and send alt when it changes.. but this is extremely convoluted, and slightly useless (it wouldn't work if you hold the key..)
Do you really need the caps lock key in other applications?
If so, perhaps you could write an AppleScript to toggle the Caps Lock key mapping? For example, in pseudo-code:
if frontmost application == "Aquaemacs":
keys.capslock = "Meta"
keys.capslock = "Default
Shouldn't be difficult using AppleScript, the code from this Apple support thread should be a good start:
tell application "System Preferences"
set current pane to pane "com.apple.preference.keyboard"
tell application "System Events"
tell application process "System Preferences"
click button "Modifier Keys..." of tab group 1 of window "Keyboard & Mouse"
tell sheet 1 of window "Keyboard & Mouse"
click pop up button 1
click menu item "No Action" of menu 1 of pop up button 1
click button "OK"