I have the GOG.com version of the game. Installing the game and running it, it works fine. When I run and install SS2Tool v5.0, I get the window "System Shock 2 has stopped working".

I have reinstalled the game twice and tried again, same thing. I installed both directx9 and vcredist before doing anything else. I have applied no mods at all, just SS2Tool.

Extra information from that window:
Problem signature:
  Problem Event Name:   APPCRASH
  Application Name:   Shock2.exe
  Application Version:   1.0.0.0
  Application Timestamp:   505eebf5
  Fault Module Name:   Shock2.exe
  Fault Module Version:   1.0.0.0
  Fault Module Timestamp:   505eebf5
  Exception Code:   c0000005
  Exception Offset:   000a8ceb
  OS Version:   6.1.7601.2.1.0.256.48
  Locale ID:   7177
  Additional Information 1:   0a9e
  Additional Information 2:   0a9e372d3b4ad19135b953a78882e789
  Additional Information 3:   0a9e
  Additional Information 4:   0a9e372d3b4ad19135b953a78882e789

Also my ss2tool.log contents:


Code:
SS2Tool 5.0.0.0
Checking if Microsoft DirectX End-User Runtimes (June 2010) is installed
Microsoft DirectX End-User Runtimes (June 2010) is installed
Checking if Microsoft Visual C++ 2008 SP1 Runtime is installed
Microsoft Visual C++ 2008 SP1 Runtime is installed
GOG.com game version detected, applying compatibility fixes
Delete file: D:\System Shock 2\allobjs.osm
Delete file: D:\System Shock 2\iface.crf
Delete file: D:\System Shock 2\intrface.crf
Delete file: D:\System Shock 2\mesh.crf
Delete file: D:\System Shock 2\obj.crf
Delete file: D:\System Shock 2\readmep.wri
Delete file: D:\System Shock 2\strings.crf
Delete file: D:\System Shock 2\SHOCK2.GAM
Delete file: D:\System Shock 2\Doc\al_reverb.ini
Delete file: D:\System Shock 2\Doc\cam_ext.cfg
Delete file: D:\System Shock 2\Doc\cam_mod.ini
Delete file: D:\System Shock 2\Doc\dbmod-sample.dml
Delete file: D:\System Shock 2\Doc\dromed.cfg
Delete file: D:\System Shock 2\Doc\fm.cfg
Delete file: D:\System Shock 2\Doc\fmsel-minimal_src.zip
Delete file: D:\System Shock 2\Doc\FMSel.pdf
Delete file: D:\System Shock 2\Doc\fm_selector_api.txt
Delete file: D:\System Shock 2\Doc\kbd_00000407.ini
Delete file: D:\System Shock 2\Doc\kbd_0000041d.ini
Delete file: D:\System Shock 2\Doc\material-format.txt
Delete file: D:\System Shock 2\Doc\modders_notes.txt
Delete file: D:\System Shock 2\Doc\mtl_incidence.jpg
Delete file: D:\System Shock 2\Doc\new_commands.txt
Delete file: D:\System Shock 2\Doc\new_config_vars.txt
Delete file: D:\System Shock 2\Doc\script\Debug.txt
Delete file: D:\System Shock 2\Doc\script\Engine.txt
Delete file: D:\System Shock 2\Doc\script\Object.txt
Delete file: D:\System Shock 2\Doc\script\Physics.txt
Delete file: D:\System Shock 2\Doc\script\ShockOverlay.txt
Delete file: D:\System Shock 2\Doc\script\ss2sample-osm.7z
Delete file: D:\System Shock 2\Doc\script\ss2_overlay_sample.cpp
Delete file: D:\System Shock 2\Doc\script\Version.txt
Remove folder: D:\System Shock 2\Doc\script\
Delete file: D:\System Shock 2\Doc\script_services.txt
Delete file: D:\System Shock 2\Doc\ss2-material-mod-sample.7z
Delete file: D:\System Shock 2\Doc\uvmap_cylinder.jpg
Delete file: D:\System Shock 2\Doc\uvmap_cylinder2.jpg
Remove folder: D:\System Shock 2\Doc\
Delete file: D:\System Shock 2\7z.dll
Delete file: D:\System Shock 2\cam_ext.cfg
Delete file: D:\System Shock 2\cam_mod.ini
Delete file: D:\System Shock 2\fmsel.dll
Delete file: D:\System Shock 2\lg.ini
Delete file: D:\System Shock 2\lgvid.dll
Delete file: D:\System Shock 2\patch_ext.crf
Delete file: D:\System Shock 2\SHOCK2.EXE
Delete file: D:\System Shock 2\command2.mis.dml
Delete file: D:\System Shock 2\earth.mis.dml
Delete file: D:\System Shock 2\hydro1.mis.dml
Delete file: D:\System Shock 2\hydro2.mis.dml
Delete file: D:\System Shock 2\station.mis.dml
Creating mod folders
Create folder: D:\System Shock 2\DataPermMods
Output folder: D:\System Shock 2\DataPermMods
Extract: !Place your mods here.txt
Create folder: D:\System Shock 2\DataTempMods
Output folder: D:\System Shock 2\DataTempMods
Extract: !Test your mods here.txt
Installing custom install.cfg
Output folder: D:\System Shock 2
Delete file: D:\System Shock 2\install.cfg
Extract: install.cfg
Delete file: D:\System Shock 2\BINDS\CFGA0000.BND
Delete file: D:\System Shock 2\BINDS\CFGA0001.BND
Delete file: D:\System Shock 2\BINDS\CFGB0000.BND
Delete file: D:\System Shock 2\BINDS\CFGB0001.BND
Create folder: D:\System Shock 2\Binds
Output folder: D:\System Shock 2\Binds
Extract: cfga0000.bnd
Extract: cfga0001.bnd
Extract: cfga0002.bnd
Extract: cfgb0000.bnd
Extract: cfgb0001.bnd
Extract: cfgb0002.bnd
Output folder: D:\System Shock 2
Extract: user.bnd
Checking if OpenAL is installed
OpenAL is installed
Adjusting settings in cam.cfg for OpenAL
Output folder: D:\System Shock 2
Downloading NewDark 2.4 patch from Systemshock.org
Output folder: D:\System Shock 2
Extract: 7za.exe
Installing NewDark 2.4
Execute: 7za.exe x -y newdark.7z
Delete file: D:\System Shock 2\newdark.7z
Delete file: D:\System Shock 2\7za.exe
NewDark 2.4 is installed
Downloading Mission DML fixes from Systemshock.org
Output folder: D:\System Shock 2
Extract: 7za.exe
Installing Mission DML fixes
Execute: 7za.exe x -y misdml.7z
Delete file: D:\System Shock 2\misdml.7z
Delete file: D:\System Shock 2\7za.exe
Mission DML fixes is installed
Completed
Creating log file

I got a mail from GOG yesterday, indicating that they changed their version of the game. From what I heard it is not updated with SS2Tool 4.0 anymore, but only with NewDark 2.4.

Due to this change SS2Tool 5.0 is most likely not compatible with the current GOG version. I will try to re-establish compatibility with the next SS2Tool version. But I'm currently on vacation in Turkey. Therefore the next SS2Tool version will not be released before next week. Until then there are two things you can do:

1. Use GOG's older installer that they served until 19th March 2013. SS2Tool 5.0 is fully compatible with that. You won't miss out on any new features by using this older GOG installer (since their update is a downgrade).

2. Experimental: If you already upgraded your GOG installer and don't have access to the older installer anymore, try installing it and then rename the file gog.ico (to whatever you like) before applying SS2Tool 5.0. The game will then be treated like a standard CD game. Might work.

If you are wondering why GOG would do this: The abridged version is that they had previously used SS2Tool 4.0 without permission. I offered them permission on the condition that they legally allow their customers to mod their games (see GOG's EULA). From what I heard from them they are still negotiating this but for now they will apparently rather abstain from SS2Tool than to allow this.

haha what? why would they try to stop people from modding? ridiculous.

Probably not their decision, I have a feeling it's a decision on the part of the insurance company they got the rights from.