are you suggesting that the patches wont work for GOG versions or do i misunderstand you? in that case I'd say: WTF??!!! does it mean I have to download all the game again everytime a patch is released??
No. Patches work, but the GOG version has a different 1.1 than other versions because it was the only version without DRM to begin with and the normal 1.1 patch strips out the DRM for the other versions. Because of that, after 1.1 all versions are identical and all patches work with all versions equally.
How far do you want to update? The latest patch is 3.3, and updating that far means updating to the Enhanced Edition (which is free, but a 12 gigabyte download, in which case it'd probably be faster and easier to just download the updated install files that currently install version 3.0).
Here's the GOG 1.1 patch: GOG 1.1
And since a bunch of patches disappeared last I checked, here are 1.2, 1.3, and 1.35: 1.2 1.3 1.35
Beyond that you're looking at version 2.0, which is a ~900 MB download, followed by the much smaller 2.1, and then the massive Enhanced Edition patch and a few smaller patches after that (well, 3.3 is ~384 MB, but it's totally unnecessary).
All things considered, I'd just download the updated installer if you want to update all the way. It'd be around the same size to download in the end, and with much less that could go wrong.