For starters, the 3.8 has a 90 degree bank angle, the 3100 has a 60 degree bank angle. 60 degrees is supposed to be the optimum for a V6, which is why it doesn't need balance shafts like the 3.8, because it was really a V8 in its former life. 90 degrees is optimal for a V8 engine.
The early 3.8 engines were odd firing, but in the early 80's, GM changed it to even firing.
The 3100 is a sequential firing order (1-2-3-4-5-6).
The early 3.8 engines were the first to get tuned sequential port fuel injection. At the time of the Series-I 3.8, the 3.1 engine, (which was 2.8 litres at the time) only had multi-port fuel injection. Basically at the time the 2.8/3.1 engine all the injectors fired at the same time, but the 3800's injectors only fired when the intake valve opened, (or slightly before). But I think currently all GM's engines have SPFI.
Basically all the "high-tech" stuff got developed on the 3.8 first, and later applied across the board on other engines. Like the roller rockers, micro-finished cylinder walls, etc.
Hopefully I interpreted your question correctly. All this information was retrieved from gmpowertrain.com a few years ago, when I used to argue with people why DOHC engines are NOT automatically higher tech than OHV engines.
bryan