Hello, I bought the square enix bundle which is just a repackaging of the gog releases. I tried running the game from the shortcut (it uses dosbox automatically) and it gave me a blue screen.

OS: Windows Vista Home Premium fully updated
My laptop is a Sony Vaio VGNAR71M with the following specs:
CPU: Intel Core 2 Duo T8100 2.1GHz
GPU: Nvidia GeForce 8400M GT (Driver version : 7.15.11.6760) (latest) 256MB
RAM: 4 GB DDR2
No firewalls, no anti-virus programs installed

As it blue screens, I can't really find any crash reports on it. Where do you think a report should be? I can't find a crash report on the tomb raider directory.
Thanks in advance.

Try this - http://www.nirsoft.net/utils/blue_screen_view.html

Dunno, not an expert on BSOD, but you can look here or just google for more results. ;)

https://answers.microsoft.com/en-us/windows/forum/windows_vista-system/bsod-caused-by-ntkrnlpaexe/a37f0b5d-c3e6-41a6-8d5b-7a84384f8820
https://answers.microsoft.com/en-us/windows/forum/windows_vista-performance/win32ksys-blue-screen-crash-on-vista/c81befb1-07d4-4863-8852-fc84cd622937

I think it's now worth trying this installer version I just posted
@ tombraiderforums.com
in the "tomb raider" section of the forums
the thread called: New version of my TR1/UB dosbox installer
on page 39
see post #389 for the link
which ought be perfectly gog-compliant

the mate who tested it reported it worked for him

Thanks for your recommendations , I'll try to fix this problem with MS and will post here as soon as I have it stop bsoding. Even when it wasn't bsoding it wouldn't run. The only time it ran is the first time I installed it and it had controller issues on the menu whenever I used a logitech rumble pad 2 lol. I wasn't able to go past the menu screen even then though. And the menu kept spinning whenever I had the rumblepad connected.
I'll post a reply to this thread as soon as the blue screen issue is fixed (if it's fixed) I'll try gidierre's solution as well. (I tried to register in your tomb raider forums twice but no evaluation of my account arrived)

I have already wasted two days with this, so prepare for this to take a long time lal.

I already posted a solution for this - http://www.gog.com/forum/tomb_raider_series/does_this_game_work_with_a_controller

I had tried that and blue screen occured for the first time :/

The microsoft forums did try to help, but with no results. I'll try to run it directly.
EDIT: Running it directly worked!
Here is how I did it:

#1
I used the GOG image file (game.gog) copied it to a simple directory I made with no spaces (e.g. C:\dosgames/tr1)
Then I renamed it to .ISO and also copied the other files in the TOMBRAID folder (the exe etc) and mounted the whole folder on dosbox directly. (just drag and drop the folder to your dosbox shortcut and it will do it itself)

#2 Proceeded to mount the image file (I named it TR1.ISO) with the command imgmount d "x:\path\TR1.iso" -t iso
#3 Now that the image file is fully loaded on dosbox, all you have to do is type the name of the .exe, i.e. type "tomb.exe"
#4 Play the game.

Please mark this as solved :)