The GS-R (B18C1) head is a different casting than the B16A head (which is also used by the Type R's B18C5 or B18C Spec R engines). The GS-R head has a smaller combustion chamber which will result in higher compression, all other things equal. There's also different cam and VTEC characteristic for a GS-R (4400 rpm VTEC point and the 2-stage intake manifold being big ones) that can be changed with aftermarket or upgraded stock parts but then would also need to be tuned specifically for the new parts.

Some people say the B16A head is "better" and the ability to use the ITR intake manifold was a huge benefit. With the Skunk2 version (the B18C1 has a different intake manfiold bolt pattern) and availablity of alternative IM (like the Edelbrock VictorX), it's a more level playing field now a days. I've always thought since the B18C1 was released in '94 and the B16A's have been around since '89, the newer head would be superior but I don't have hard facts to back it up. I would think cam choice and tuning would be a larger factor than which head is bolted to the engine.