Indeed, a very good point.

SecuRom:
Online Retailers
* Boonty
* Digital Interactive Systems Corporation
* Digital River, Inc.
* Exent
* Gamersgate AB
* GameStop Corporation
* GameStreamer, Inc.
* IGN Entertainment, Inc.
* Metaboli SA
* Nexway
* RealNetworks, Inc.
* Ztorm AB

Fan patches typically don't alter the executable file. Doing so would make the patch about as legal as the average nodvd patch. It's the game's main exe that would contain the disc check (which as Coelocanth rightly points out isn't always present, but it is far more often than not).
Fan patches usually rely on official patches to fix any problems in the executable and usually require an updated version of the game as a result.
So considering that the vast majority of GOG games are already patched to the latest version, fan patches shouldn't be affected.

Well given his next port (the one I quote below) he seem to think that the game remained DRM-free even after being update which it not the game. (Which is pretty silly if you ask me as some non-Stardock impulse games are really DRM-free and remain DRM-free even after update like Braid for exemple)
Wrong
That was exactly my point, as soon as you update the game it's no longer protection/DRM free if you backup the folder and try to play it on another computer (or even if you change something on your computer or reinstall windows) you will be forced to reactivate the game online.
Actually, "before" things were working as you said and games remained DRM-free even after updates but apparently they changed this behavior some months ago.

O RLY?!
I'll have to check this out. I ran it fine off another OS without reinstallation and I ran it at the newest version. And this wasn't too long ago. I dunno why they would change that behavior though, since the only reason you would want to patch is for MP, which obviously requires a valid account and such.

Wanting to buy Bioshock on the D2D sale, but never used it before. any issues i should know about?
I'm ok with things like steam, but i don't want too much junk installed on my PC.
Also, bioshock originally had activation limits/securom, but i've heard they've been disabled... any dangerous parts still hanging around?

The only things hanging around are euphemisms for penis. Sorry.
Seriously though, you should be fine. Look around on the 2K forums for Bioshock DRM scares and if people are generally happy with the D2D version, then it should be fine.