The basic differences between the 029 and the 029 super are:
(1). The super has a 1mm larger piston and cylinder (029 super is 46mm, 029 is 45mm).
(2). The super has a fully compensating carb - versus a non compensator on the 029.
(3). As has been stated the 029 or the super are candidates for the 039/MS390 swap on the motor assembly --
I just finished one recently and am very happy with the upgrade.
That being said, I have owned and do have all three models. If I bought an running 029 I'd simply do a muffler mod and let it roll.
If I bought a running 029 super, I'd pull the limiter caps from the carb, mod the muffler and let it roll.
If I bought a 029 or 029 super that was toast - it might be hard for me NOT to buy the parts and/or the MS390 Bailey's option.
My 2 pennies...
Happy Sawing!