So I'll keep this short and simple, the only real games I can run with any sort of stability are games that run in DOSBox or really low-spec games. I opt for the former, but I'm having a bit of trouble figuring out the best way to "extract" or install DOS-based GOG games to run in DOSBox or any applicable Linux version of it (running Ubuntu if that helps cut down my options). Most already supported titles like Master of Orion or the DND games seem to work without any issue, but a few games that aren't supported (like Wing Commander, SimCity 2000, Theme Hospital, Space Quest, X-COM etc) are my 'white whales'. Any help would be extremely appreciated!

I usually do the following:
1) Install the game using its Windows installer under Wine
2) Copy the game directory or the subdirectory (depends on the game here) somewhere else - a folder I've created for my DOSBox games
3) Look at the .conf files packaged with the Windows installer - there will usually be two (or more, but two will be enough for getting single player started): one that contains the general DOSBox configurations for the game and another that contains the autoexec part for launching the single player game
4) Mash the two .conf files into a single .conf file and adjust game paths as necessary (you may need a couple of tries here, especially if there are mount commands in there as well), and adjust any other settings (set fullscreen if you like, adjust the renderer, audio sample rate etc.)
5) Launch the game using: dosbox -conf your_new_conf_file.conf

For WinterSnowfall's point #5 above, you add those to the link you want to start the game with. (Right click on link, Click edit properties.)

For step 1), another option is to use innoextract from the terminal, which forgoes installing the game with wine. It should be available in ubuntu software repository.

Okay - I'd followed the steps with one game: SimCity 2000. Results are kinda mixed, had to configure the sound a few times and got it working but upon closing the game out It loads me into the DOS prompt with "Now leaving SimCity 2000" and none of my inputs work. Not even alt-tabbing. To fix it, I put DOSBox into fullscreen from a window which for some reason crashes it out, and leaves my resolution wonky but I'm able to fix that.

Any way to keep it from crashing or to keep it from messing with my resolution?

./play.it might be a solution you’d like.
It’s not a launcher or anything like this, but a lightweight software that builds native packages from game installers, including some GOG games. So you would end up with .deb packages ready to be installed on your Ubuntu machine.
Once your game is installed, you no longer needs ./play.it to run it, it’s only used to ease the installation and initial configuration process.

Starting with Ubuntu 18.10, ./play.it is included in the official repositories and can be installed with: We try to tweak the games configuration when needed to ensure they run smoothly on a wide variety on systems, but of course we may miss some bugs ;) If you spot one of them please report it in the thread I linked in this post.

List of DOSBox games supported by ./play.it
List of ScummVM games supported by ./play.it

Absolutely looks worthwhile, going to try later tonight and report back any success.

I use Lutris, it's an open source games launcher. While it's a bit lacking on the side of Dosbox configuration, it is better than not having organization at all.

I had been using DBGL, but with the fickle nature of Java/OpenJDK, that's no longer an option.

I can try that as well. the Play scripts for some Windows games worked fine but it looks like PlayOnLinux and Lutris can carry some weight too.

Play on Linux mostly just carries laughably old versions of Wine.

Even if so I've had luck using it to get a few games working. Even still, Lutris, PoL and the .play scripts are a pretty good set of tools given with that I've gotten 90% of my GOG library running without a lot of issue.

Nice ;)
Feel free to share the names of the remaining 10%, maybe some of us can help in getting them to run too.

Sorry for the late reply. For those few games where you have to start things using .bat files, using call usually gets you out of any wierd situations on exit.

Here's what I have in my Simcity 2000 DOSBox conf file under the [autoexec] section:

[autoexec]
# Lines in this section will be run at startup.
@ECHO OFF
mount c: SimCity_2000
c:
imgmount d "SC2000SE.DAT" -t iso -fs iso
call SC2000.BAT
exit

As to the resolution, you can use fullresolution=desktop sometimes, which will stretch the game to the resolution you're currently using, but it won't always look pretty and won't always work. Other times games won't work at all unless you go down this route. Dungeon Keeper I believe is one of the few games that only work with this setting in effect.

An alternative would be to have screen resize scripts ready in the upper left corner of your desktop :D. Call me a barbarian, but that's how I do it. Here an example for 1080p:

xrandr --output `xrandr | grep " connected"|cut -f1 -d" "` --mode 1920x1080 --scale 1x1 --panning 1920x1080

Unfortunately their all Windows based, or have issues in other departments - like Interstate 76 with it's FPS bugs, Archimedean Dynasty just for some reason having low frames in regular DOSBox, with the bundled version or under WINE (I think I got that spelling correct lol) and Blood 2 (although between you and me I'm not losing sleep over that not running).
I mean, shoot if you can help I'd appreciate it but 90% is still an A- lol.
I'd tried your method and I'm still having issues. Although this time I just hit CTRL-F9 (or ALT-F9? still at the office can't recall 100%) and it'll kick me out and shut off DOSBox but my resolution remains stretched and zoomed in if the 'fullscreen' command works at all.
I'm currently stuck with a Laptop running around 1336x768, and even in my native DOSBox I can't get the resolution to alter. This is using the dosbox-jz version available on the Ubuntu software repository, I dunno if DOSBox-X can give any extra help or not. Although I'm willing to try.

This method however DID fix a mouse issue and my sound not playing correctly so I'm going in the right direction.