Just bought System Shock (hey, its got a plot that could be straight out of a William Gibson novel, how could I not like it :) and want to know if there are any guides for newbies to the game out there?
Especially in regards to the controls which are different to any FPS I have ever played (classic or modern) and in to just what it is that I am supposed to be doing in this game...

see the newbie guide here.

the last fella posted a SS2 guide... I think you refer to System Shock 1 right?

The basics on the controls are on the new manual, there's a new page that details the new functions (like pressing e for mouse look) once you get used to press e to enter in "FPS control mode" and press it again to go in inventory management mode it will all make sense :)

Also fundamental part of enjoying this title is the awesome ambient music, make sure you load a nice soundback to replace window's default one and if you get stuck use the included hint guide!

You may want to scroll down.

haha you right!
I tought the link was exclusively about SS2 info :p
I check it and it's loads of info on Shock Portable and SHlink but I didn't need that to play GOG's version... I know GOG's is using a form of the Portable version (the only way to run the game on modern windows until recently..) but I just wanted to make thinks a tad simple for the OP :)