I found a software called AutoHotkey which enable custom configuration on the keyboard. All you need is install the software. After that, open your notepad and fill in with this code:
LWin::LAlt
LAlt::LWin
What it does is swapping both key. Save it as win-alt.ahk
Double click on it to activate.
You can choose to put the file in the startup folder to let it run everytime you boot windows.
Now, get back to dota and time to own.
*Update on 09 January 2009
I've found a new software called keytweak which basically does same thing, but more native and less buggy, because keyTweak tend to manipulate keyboard registry value.

As you can see above, the concept remained the same, this is quite easy to achieve.
Just click full teach mode, and begin the key mapping, basically you have to do it twice, by swapping both of the key. Failing to do so will only replace a key and not swapping them.
