Inny: Well... isn't GoG supposed to remove copy protection on his games ?
GoG removes DRM - generic copy protection systems that prevent you installing multiple copies, running the game without the cd, etc. These methods usually have their own code separate from the code of the game itself (because they're licensed by the developers from a separate company like starforce or securom).
Old-fashioned 'check the manual' protection methods were programmed by the developers themselves on a per-game basis, so they're harder to identify and remove since they're in with the rest of the code and can be completely different between different games.
They are a bit of a pain, but the internet and PDF manuals mean they're less of a bother than they were when they were originally released - you could say that they never actually prevented copying, just made it harder since you needed to copy the info from the manual too.
It will be interesting to see how GoG deals with a 'code wheel' protection system when they get a game that uses one - some of those can have hundreds of combinations so you can't just look them up in a list, although I have seen them done with Java or Flash.