This is more of a nitpick than a problem, but is it possible to configure ROTT to exit out to the DOS prompt instead of it automatically going back into Windows? I like reading the big "Thank you for playing X!" text boxes because it brings back a big sense of nostalgia to the game. =)
I know with Duke Nukem 3D, all I had to do was take the "exit" perimeter out of it's shortcut and the exit command out of the bottom of it's .CONF file, but ROTT uses a new gogwrap.exe to run the game and it still comes back to Windows automatically when I exit the game even though I took "exit" off of the shortcut path and out of the .CONF file.

You could try getting DOSBox separately and launching the game through that, DOSBox won't close automatically that way and you can see the message.

Well, I made a different shortcut going around the gogwrap.exe with these shortcut parimeters and I made a simple mistake that was causing it to not launch:
"C:\Program Files (x86)\GOG.com\Rise of The Triad\DOSBOX\dosbox.exe" -conf dosboxRiseOOT.conf
Notice something? The reason why that wouldn't work is because the .CONF is named dosboxRiseOTT.conf instead! Sooo yeah...pardon my dyslexia.
Thanks for your help though guys, I appreciate it! =)
This is the screen I was talking about, by the way:
http://i40.tinypic.com/20pxyeg.jpg
Yes, I'm a nerd. =P
Good to see it again, and it's awesome to play this again! I still have my original CD and manual, but I bought it on here again to give this great site the support.

For technical reasons, please pick an answer to resolve this thread. The topic will then appear as "solved" in the topic list and as a valid answer in the support section.

If you open up Regedit you can fix the commands given to the GOGWrapper so it dosn't close DOSBox on game exit
Under HKEY_LOCAL_MACHINE\SOFTWARE\GOG.com\GOGROTT\
You should see two lines
One Called DOSBOXPARAM
Wich has the following default value [ -conf dosboxRiseOTT.conf -noconsole -c "exit" ] (without the [ ] )
change that to [ -conf dosboxRiseOTT.conf -noconsole ]
(without the [ ] )
The second value is called LAUNCHCOMMAND
It looks like this if you chose that you already installed DOSBox during ROTT's installation
[ "D:\Programmer\DOSBox-0.72\dosbox.exe" -conf dosboxRiseOTT.conf -noconsole -c "exit" ]
(Without the [ ] )
Change that line so -c "exit" is removed..
Then you should be able to run ROTT through gogwrap.exe, without it closeing DOSBox after game exit..
This can also be done with other DOSBox powered games from GOG