One of the major selling points for GoG games is that they are optimized for XP and Vista. I like this because I dont really know how to use DOS Box and it's convenient to not have to learn.
I was thinking about this though... in like 10 years from now, if I want to play these same games on whatever Operating System is in place in the future, will the custom GoG installs make it harder to get these games to run than if I was just working from the original non-gog version of the game?

Yeah, keeping older games playable on modern systems is kind of the foundation of the entire business. Or at least a major part of it.
But I suppose that in the far, far future, your old setup file will not be very cooperative, no. And maybe, in some cases, it would be at least as much trouble to get running as the original game. But I wouldn't know for sure, I don't know very much about the magic the good people at GOG practice.

Good question, yeah, for the long long term. Something I've wondered.
I'm thinking by then something like DOSBox will have been made for this era of gaming and that'll take care of that. GOGs programmers seem to know their stuff very well, and the community always comes up with something. I have no doubts.

Let's just hope that Windows 8 and 9 have better backward-compatibility in terms of gaming...

Might also be worth while considering keeping around an XP machine for old gaming in the future. Its hard to tell what the tech will be in 10 years time so if you keep the system yourself your gaurenteed to beable to play what you can now in 10 years.

That's exactly why I still have an old machine with Windows 98 right now. I don't really use it much, probably haven't even turned it on in about a year, but it is always there just in case.

I wish I had kept a windows 95 machine in good nick for myself, I had 5 of them on a lan at one point but I didn't look after any of them properly. I still have my 166 but there are a couple windows 95/98 games I just can't get running on xp that I'd love to play again. Hopefully gog will pick them up at some point and sort em out.

Even if a time comes when Windows can no longer run the GOG installers natively it would be easy enough to run them through a virtual machine (such as Microsoft's own Windows XP Mode available for Windows 7 Professional, Enterprise and Ultimate). I have been doing this already for older Windows games with 16-bit-only installers and it works just fine.

The only problem with VMs is that you get the most generic of video drivers, usually something akin to an S3 Trio

GOG will continue to add support for their installers in each new 200$ release of Windows(tm). Right now they are working on Windows 7 support, for example.

Thanks for the responses. I voted domgrief as the solution because I guess I was ultimately wondering if the GoG installers would be better to have in the future than the standard install.
The idea of using a virtual desktop with a different OS is also a good idea.

ideally you'd be able to extract the files with an archiver program like 7-zip or similar..
I've run across many cases where I've had to use various extraction utilities for different game installers over the years due to hardcoded restrictions, bugs in the installers, loss of support for the installer or 16bit installers.
Hopefully GOG will change their ways in the future or support will be included in Universal Extractor\ 7-zip or the like to extract the files.
If you are really worried about it then best bet would be to install the games right now using a Software Virtualization programs like Symantec Workspace Virtualization. Then you'd be able to backup the changes it makes to your registry and note exactly where files are placed and back them up as well. Zip them up using 7-zip using the STORE compression level in .ZIP format for best compatibility for the future. (May want to make an MD5 hash while you are at it).