The main difference between a GM 12 bolt rear end, the Ford 9" rear end and the Dana 60 rear end is the size (and strength) of the ring gear. The 12 bolt rear end has a 8.875" ring gear, the Ford 9" of course has a 9" ring gear and the Dana 60 has a massive 9.75" ring gear. Obviously, the strongest rear end is the Dana 60.
Which do you need? That's a question we get asked often, and there's really no right answer. It mostly just boils down to preference. We'll give you a few opinions to guide you.
You don't want a rear end that is any bigger and heavier then what you need. If you have a car making 450 RWHP, you don't need the added bulk and weight of a Dana 60. Many GM guys refuse to put a "Ford" product under their car, and that's cool too. If you have a street/strip car making under 700 horsepower the 12 bolt will serve you very well.
If you have over 700 horsepower, then we'd recommend a 9" or a Dana 60. The 9" is very easy to work on and can be easily disassembled with simple hand tools. It's also very easy to pull the center section in and out for guys who want to run different gear ratios depending on what they're doing with the car, another big advantage to the 9".
The Dana 60 is a monster, if you have a big horsepower car then you can't go wrong with the Dana 60, drop it in and forget about it.