I..y..no.

I guess I should have explained that you should only have one of the outputs. I put them all there so you could choose which one.

Yeah, you were meant to pick one of those. XD

My preferred one is output=ddraw.

I tried to do that. This is what happened

I opened the file (had to manually select notepad as it didn't already open with it) I made the changes. Tried to save, but it said I didn't have permission. The file doesn't have an option to run as administrator.

It just wont let me save it. I have a resolution of 1366x768 and in game the menu is completely offscreen. Is there any way to fix this

same here... barely fits half the screen. =( Tried to revert the .conf file with fullscreen : true...but it doesnt change back.. sigh

Contact Support.

I too suffered from the square picture with the gapping and annoying black side bars.

None of the above suggestions fixed it, so I decided to dig into the options myself. After a long and frustrating afternoon, I found the following code that allowed the game to use my whole screen with no more annoying side bars.

Go to C:\Program Files (x86)\GOG.com\Theme Hospital and edit dosboxTH.conf

note: I just re-installed this on 4/21/2016 and the above path had changed on me...If you can't find the above, try this:
C:\Program Files (x86)\GalaxyClient\Games\Theme Hospital

Replace this code block:

fullscreen=true
fulldouble=false
fullresolution=desktop
windowresolution=original
output=overlay
autolock=true
sensitivity=100
waitonerror=true
priority=higher,normal
mapperfile=mapper.txt
usescancodes=true

with this:

fullscreen=true
fulldouble=false
fullresolution=original
windowresolution=original
output=surface
autolock=true
sensitivity=100
waitonerror=true
priority=higher,normal
mapperfile=mapper.txt
usescancodes=true

Hope this gives you as much happiness as it did me. :)