For the impatient: download Estonian3.keylayout.zip
Unzip and put the two included files into
~/Library/Keyboard Layouts/ folder. (NB! Few people have indicated that with Snow Leopard or Lion this layout creates some issues with input, but a restart will fix those.)
The Mac OS X version of Estonian keyboard layout and localized version found here, both lack the caret ^ symbol (in its usual place). Also I had an external HP usb keyboard, which again was incompatible with the internal keyboard (the ~ and | symbol keys were swapped). This was a big issue for me, because I often use both of them in scripts.
So, I turned to Ukelele and configured my own layouts.