EDIT Rewritten 15/02/14 for more complete and concise instructions.
Mods for STALKER games are quiet patch version dependent. The GOG version of Shadow of Chernobyl comes pre-patched to v1.0006. This patch wasn't widely used by the modding community for various reasons. So to play a large number of mods you will need to downgrade your game to either v1.0004 or v1.0005.

To downgrade to v1.0005 you need to download the US v1.0005 patch which can be found here.
www.gamershell.com/download_21947.shtml
Note: You MUST use the US version! All other versions of the patches still contain the DRM(disk check). ONLY the US version is DRM free. The WorldWide patches will mess up your XR_3DA.exe and the game won't run without a disk, which you obviously don't have ;)

Once you have it you'll have to change some registry values
Warning: Please DO NOT edit anything in the registry unless instructed to do so. Incorrect editing of the registry can seriously damage your OS. Requiring a complete re-install to fix!

1. Press win key + R and type "Regedit" hit ok.
2. Navigate to Path: HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\GSC Game World\STALKER-SHOC (For 64-Bit systems, 32-Bit seems to be missing the Wow6432Node subfolder, but haven't tested this)
3.Change the following values by right clicking on the heading and selecting modify, then clicking OK
(See Screens)
- InstallLang = en
(Is case sensitive! The patches install language)
- InstallVers= 1.0004
(This tricks the patch into thinking you have v1.0004 installed)
- InstallSource = stk-for-pack-noprot-efis
(This will make sure that the installer will recognize a US version of the game which will allow you to install the patch)
Close the window.
(All settings are saved on exit)

Now you should be able to install the US v1.0005 patch .
Note: You will get a runtime error about not being able to find the read me. Just ignore it ;)
However it will install under
C:\Program Files (x86)\THQ\S.T.A.L.K.E.R. - Shadow of Chernobyl
(At least that is what happened on my computer).
Therefore you need to copy the files manually from that patch installation directory to the GoG Install directory.

You will also need to delete the following files from the GoG Install directory based on which patch you just downgraded to.
For patch v1.0005 delete gamedata.dbd (this is installed by v1.0006)
For patch v1.0004 delete gamedata.dbb, gamedata.dbc (these are added by v1.0005)
If done correctly your game will now be patched to V1.0005 and you can install all those awesome mods :)

For downgrading to v1.0004. Just replace
- InstallVers= 1.0004
with
- InstallVers= 1.0003
and use the v1.0004 US patch.

Last of all go to control panel - programs and features and uninstall the patch.
(you don't need it installed after copying the files to the GOG game directory.)

I'd like to thank the user "TheMechanist" on the following thread for his original instructions without which i wouldn't of known where to start.
www.gog.com/forum/stalker_series/soc_v10006

Well I feel honored to be mentioned but the credit for the correct reg entrys for the US patches and the testing goes to you.
Thank you very much for testing :)
Maybe you should note that ONLY the US patch will work, because its DRM-free. There might be confusion with users from Europe who don't see the difference between [WorldWide] and [US] - since there normally wouldn't be one.
This should be a sticky until the GoG-Team comes up with a homebrewed downgrade option :)

Good Point, i'll edit the OP. Thanks

You positive it's 1.0006? I couldn't afford buying the GOG versions just for the hell of it so I'm stuck with the Steam version that I got years ago (and which is luckily patched to 1.0005). Anyway, if they actually use v1.0006 in the GOG release: I'm shocked. It wasn't just a patch that the community didn't like, it was a broken patch that the developers officially withdrew. You'd think that GOG or GSC would have known better working on this release...

Anyway, +1 for providing downgrade instructions.

Edit: Okay, something's weird. The Steam version used to be 1.0005 but it's also 1.0006 now. I'm positive that it used to be 1.0005 because that's how I even learned about 1.0006 having been withdrawn - when I last played Stalker three or four years ago it was 1.0005. Can it be that the ignorant bitching community put so much pressure on GSC that they actually decided to stick to 1.0006 after all???

I can confirm it's 1.0006 and I can also confirm the Priboi mod worked when I used the latest update that was intended for 1.0005 and not 1.0006 along with Mod Pack 2013 if I left out the dll file that was in a bin file that came with the mod.

I haven't tried a mod that requires 1.0004 however.

Yeah, Its defiantly 1.0006. Some of the 1.0005 mods will work with 1.0006 some won't. I'm currently playing a merge of:
AMK 1.4
AMK 2.0.94 Patch
AMK hot Swapper
AMK Retranslated
AMK Arsenal V1
Absolute textures( nature and structures)
Complete 2009 (just the textures and meshes)
Lurk Hand and weapon animations
Minimul hud for AMK
Shaders max
SWO + AMK patch

Its v1.0004 only though. Used the above downgrade and it works fine.
and Its pretty awesome :)

Check out "David.me" modDB page. The guys a legend. He has heaps of translated and merged russian mods for all 3 STALKER games.

moddb.com/members/davidme
(look for this section)
MEGA Download site with multiple alternate links for mods for all 3 STALKER games:
MEGA

I also believe this post should be stickied, clears up all confusion and emphasizes the differences in versions and why downgrades are necessary for certain mods. Would hate to see this post disappear off page one of this forum.

v1.0006 does seem to have at least one perk, better widescreen font scaling in 1366 x 768. I am under the impression once you into the higher resolutions the fonts look better, but for whatever reason without v1.0006 the fonts become enormous and somewhat distracting in 768p. It's not a major issue if I get to play mods like OGSE.

I created a packed archive of the installers content and exported registry hacks that go with it for both 1.0004 and 1.0005. Anybody want to be a tester? Especially for the 32-Bit hacks, since I only edited the pathes by logic explained in our tutorial ;)
This way it should be way easier for unexperienced users to downgrade. Just put the content of the wanted patch folder into your games main directory and overwrite all. Then doubleclick on the proper reg file and click on yes.
Everything should be configured nice and toasty now.
-- WARNING: This is still untested. I take no responsibility for anything that might happen. It should work though ;) --
I'm going to look for an option to make it an installer. I have no experience with this kind of stuff though :/ And it must be tested before this anyway :D Have fun!
DB Link: https://dl.dropboxusercontent.com/u/6059349/Stalker%20SoC%20Downgrade%20Pack.7z

Thank you Issar077 and TheMechanist! I had not noticed it was v1.0006 and I was running Oblivion Lost 2.2 for v1.0005. It was all going fine until I got to the Bar area, then it kept crashing a few seconds after loading.

Wonderfully, my savegames work with the downgrade in place. Thanks to you both again - now to continue my return to the Zone!

Hi, did anyone try NewMechanist automatic patcher?

One thing I wanted to say:

In the instructions, you say we have to delete gamedata.dbb, gamedata.dbc and gamedata.dbd if we want to downgrade to 1.0004. In my case, I dont have to delete gamedata.dbb, If I do this the game crashes to desktop.

Thanks for the tips!

I do not and will not use GOG - Galaxy and this created a problem for me when it comes to downgrading from 1.0006 to 1.0005.

I have both GOG STALKER installers - the one that installs the purely Russian version 1.0006 and the one that installs Multi-Language version 1.0006, which comes with separate localization folders in the main directory after the installation.

I want to play the Russian version for sure, but can US patch be used with it without it messing up Russian voices and text?

I can also try this - install the Multi-Language GOG version, and then copy Russian localization files into it. The problem is that when I install the Russian version, there are no localization folders for copy-ing!

What do I do?

www.gamershell.com doesn't have the patches available anymore. :(

I don't think this whole downgrade thing is even necessary anymore. All the mods I've tried have worked with the unmodified GOG version. Best try to run the mod first, before you try this whole process of downgrading your game version.

It's still necessary for all the old mods out there and a lot of them are excellent. You'd be missing out if you don't play them.