They are not identical, but they are very close. The Steam version has a slightly better configuration program (eliminating the need for the disk version if you want to run it in software mode rather than Direct3D), has added support for Win 7 (though the GOG version will run under Win 7) and dropped support for Win 98.
From a topic in the Larian forum;
...the version on GOG and the version on Steam are different ports due to an accident at Larian that caused us to lose the source code of the GOG version. It's a pretty stupid thing, but sometimes things go wrong. So to make the Steam version, the port to adapt for Windows 7, had to be redone. Therefore, there's no relation between the GOG version and the Steam version, other than they're based on the same original game.
We're going to look at what issues might appear if we release the Steam version on GOG, and if none show up, we'll make it available there too, just to make future updates easier.