Its not silly in the slightest, I deal with it all the time. I have Windows on its own partition and a separate partition with two directories: Applications and Games. Most of the software I install will go in either Applications or Games, but there are some things that will always go in Windows, either by preference or design. Because of that, changing the default application directory doesn't fix anything, it just means that instead of changing the install path from C:\Program Files\Blah, sometimes I will have to change it from D:\Applications\Blah. In the end, I'm still doing the same thing, so I don't see any reason to bother changing that.

Well, the reason why you do it like that is that Windows tends to barf less and you're less likely to get things installed arbitrarily between the two. Seems odd to me to segregate the games and apps, but when you put it that way, it does make a lot more sense.

OTOH, I would like to see gOg adopt a convention where they create one folder for game saves in My Documents so that it's easier to save the save games when reinstalling the OS or moving between computers.

Won't happen. At least not for all games on GOG, since that stuff is mostly hard-coded into the game.

Sometimes, save location is a function of the game code itself, so GOG can't really change that, but I agree, having a common location for all saves would be nice. Quite a few games already do that (I've got save files in My Documents for Aquanox 2, Darkstar One, the GTA games, Bioshock, Deus Ex: IW, Freelancer, Oblivion, Gal Civ 2, Spellforce, Penumbra, The Witcher, Thief DS and Two Worlds) but not all of them do or can.

OK, here it is: considering that all games on GOG go to Program Files\GOG.com here's a script that symlinks that to a new folder (in this case D:\Games\GOG).

This means that all games installed in the default folder actually get saved to D:\Games\GOG and every reference to them (shortcuts, etc.) leads to the same place.

Default is the 32bit code. To switch to 64bit just edit the file with a text editor and follow the instructions in the comments.

To switch the install directory to something else just edit the file with a text editor and follow the instructions in the comments.

This script works on Windows Vista and 7 and must be run as administrator.

Grab the file from here.

And here's a video on how to switch from 32bit to 64 just in case the comments aren't clear.

That's true, considering the code that's being dealt with it would almost certainly be easier to write a script which backs up and restores the data. On versions which support it, they could also just link it. Unfortunately, that doesn't work with XP as far as a quick search indicates.

Although they won't rewrite games to change the save directory, they could make their installer Vista/7 friendly with the option to create a symlink. Or, you could use GameSave Manager.
It's not entirely the same, but I suppose it would make moving all saves to a new computer easier. You'll still have to manually add the save paths once though, it doesn't recognize any GOG game I have.

I'm going to give that a whirl. Looks promising.

Althou I know some GOG-games (most games perhaps) have a custom installation option not all games I´v bought have that option.

For instance I remember searching the installer for "Hostile Waters" without finding any such options. Otherwise I always choose the "options" button to choose another installation directory if its avaliable.

I've built a system up for the DOSbox based games where the games are installed in a read-only location (/usr/local/games) and using UnionFS-Fuse, all the files written go into $HOME/.gog/<nameofgame> so I just have to back up the $HOME/.gog folder.

Something similar may be achievable in Windows with some sandbox software..