Windows is infinitely more complex than DOS, and it will be a very, very long time before any Windows replication reaches anywhere near as usable state as DOSBox.
Windows emulation is already readily available with virtual machine products such as VirtualBox and Windows Virtual PC, although you need to supply your own copy of Windows (Windows 7 Professional, Ultimate and Enterprise include a free XP Pro SP3 VM license). If you have a CPU that supports AMD-V or Intel VT-x the virtualised OS can run at near-native speed (although with the obvious overhead of two operating systems running at the same time). Because the VM is running a real, fully functional version of Windows it has 100% compatibility, which no emulator or API replication could ever have.
No VM has proper Direct3D support at the moment, unfortunately, due to a complete lack of anything like the hardware-assisted virtualisation technology included in CPUs; games that use or support DirectDraw, OpenGL or software rendering will work just fine in most cases.

If the idea is to emulate early Windows games... Then wouldn't it make sense to start by emulating Windows 95? Windows 3.1 was just a GUI for DOS that DOSBox could even emulate, but Windows 95 was the first unique Windows OS. 95 also shouldn't be as complex as XP would be. Windows 95 nowadays is also a lot less common than XP, as many shunned Vista for XP.

Huh? You're not paying GOG to provide you with a free program. You're paying GOG to provide you with the game.
If you already own the game in question, you don't need GOG -- you can download DOSBox yourself and run it that way.
Early 3D graphics often means 3Dfx/Glide, and there are some excellent wrappers for converting Glide calls into Direct3D equivalents. They won't work for all games, but they do a very impressive job IMHO.
dgVoodoo is the best one that I've used, followed by Zeckensack's wrapper.
http://dege.freeweb.hu/
http://www.zeckensack.de/glide/
Glidos is for DOS-based Glide games, as the name suggests. I've not tried it myself, as it's commercial and I found the others met my needs, but if you want to play the games mentioned on the site, it's most likely a very decent choice.
http://www.glidos.net/
There are others that I know of, but I'd be a little surprised if any of them did a better job than the ones mentioned above.
https://sourceforge.net/projects/openglide
http://evoodoo.emulation64.com/us/home.html
http://www.geocities.co.jp/SiliconValley/8346/gl2ideal/
Unless you want to play Diablo 2 specifically, in which case there is this:
http://www.svenswrapper.de/english/

Ehm, I'd like to point out that DOSBox has already started to "emulate" the Windows '95 GUI :-P

sorry dosbox guys... i took it off topic.
(though its all useful info... maybe i should have started another thread. what's the situation with dual booting a copy of win95 on a modern dual core PC and slowing it down somehow? )
U guys rock.

If so many of your games are using DOSBox which seems to be compatible with a lot of other operating systems than Windows XP and Vista - why are you only listing those as compatible?
I'm using OS X and I've bought some games through gog.com - hoping that they should work on my Mac through Wine/Crossover Games but for those games that are already using something like DOSBox that wouldn't be necessary and I wouldn't need to worry if the game can be run on OS X or not - so why aren't you printing this out?
Most old games works easily on OS X, Linux and similar without any special effort and those platforms lack new exciting games - so it would be great if you could make it easier to find out which games works good on those platforms.
Perhaps work together with DOSBox and Wine/Crossover?

VoxPelli: Although the games can certainly be played on other systems, the reason is that the installer that GOG provides is a Windows-specific executable. So at present, GOG doesn't formally support any other systems.
You can, of course, run the GOG installer on a Windows box and then copy the unpacked game files from there to your Linux/OSX/BeOS/RiscOS/whatever machine, and use a native DOSBox to play it.
That presumes you have access to a Windows system, of course.
It would be great if GOG provided a simple compressed archive of the game files (along with the dosbox.conf file) as an alternative download, so that those who wish to could set it up themselves without even needing access to Windows.
That would open up a whole new audience for GOG, for quite minimal extra effort.

As a Linux/BSD user, I have to agree with Shadowcat. It would be nice to be able to retrieve the files for a game without the shackles of a Windows installer.

I've already ask them exactly about that... They've got deals for Windows platform only, so you can personnaly run them elsewhere, but they can't help you for that =(.

i don't use linux much, but it seems like a good idea, business wise.
Lots of linux gamers are desperate for games, and with the recent rise in netbooks...
money to be made...

an innosetup unpacker would be quite handy,
but fortunately the installers of GOG work pretty well in wine.
Thank you all for the praises of DOSBox!