Hi guys! First post here, so bear with me..

I recently went on holiday, and started playing one of the classics from GOG.com (Stonekeep) on my wife's laptop. I got home today and was wondering how I would go about transferring my save game onto my own laptop?

I tried copying the entire GOG.com directory over in place of my old, but when I open the desktop shortcut (which, in theory now leads to the new folder as it's replaced the old) the only save game in the load game option is my old one, which is approximately 3 minutes into the game.

Anyone have any ideas why? Any advice would be greatly appreciated

Install this:

http://www.gamesave-manager.com/

It'll make a backup of your save games that you can then take to your other computer.

Couldn't he just go through his files, copy and transfer over the saves separately?

I tried this, and for some reason it still only detected the original save game. I had 3 saves in the new folder, and it didn't find any of these.

I also installed the gamesave-manager, backed up from the wifes laptop and restored on mine and still only had the original save.

Something tells me I might need to restart >_<

Are you by any chance using Windows Vista/7 on any of the two computers, and have installed the game in Program Files?
If yes, there is a chance that the actual saves are located in the virtualstore directory.
Will post more details in a few minutes.

I am using Windows 7, yes. Virtualstore directory.. sounds complex!

Ok, let's start with the basics, which should cover Stonekeep as well, though not 100% sure about this.
In Windows Vista and later, system folders (c:\windows, c:\Program Files, etc) require elevated permissions to be modified. Even if your user is set as an administrator, the system will be asking you to "run as administrator" if you want to modify something there.
A lot of games want to write something to their folder, which they can't, so Windows uses a special directory for those writes. The directory is located in "C:\Users\{username}\AppData\Local\VirtualStore", where {username} is your windows username. Navigating there, you will find a "Program Files (x86)\GOG.com\Stonekeep" folder, which should contain your saves.
The problem usually is that when you run the game as a user, it will use the virtualstore directory, but if you run it as an administrator it will use the program files one. So, check that the saves from the laptop are taken from the correct directory (if using XP then they will be in the Program Files, if using Vista/7 they'll probably be in the Virtualstore one), and copy them to the equivalent on your desktop.
Also, highly recommended is to not install any game in the Program Files directory, for the above reasons.
Hope this is not to complicated, if you need to ask anything else, feel free.