Here is how you can set a custom windowed resolution for SimCity 4:

Go to the main game directory (usually "SimCity 4 Deluxe Edition") and find the "Apps" folder. Create a shortcut to the SimCity 4.exe file and go to its Properties (usually by right-click). In the Target field type this in after the exe file:

-CPUcount:1 -w -intro:off -CustomResolution:enabled -r1024x768x32


The "-CPUcount:1" is only needed for computers with multi-core processors and the "-w" command enables windowed more. The "intro:off" command will disable the intro so it won't have a negative effect on the window. The "-r" command will set the custom resolution. You can type in any resolution, but I would suggest using a 4:3 ratio since the game wasn't necessarily made for widescreen.

Actually the game was perfectly designed for custom resolutions, it technically has native widescreen support. Also all GUI elements are properly aligned at 16:9 resolutions so I really don't know what you're talking about.

I noticed the pre-set full screen resolutions in the game were pretty limited. That's why I had to search for a CustomResolution command.

Thanks, GOG, for your version. Origin version is broken now in terms of custom resolutions.

More specifically, it's necessary because the game will crash at random otherwise.
The devs probably expected multicore processors in the future and implemented support for it, but since none of the testers had access to a multicore or multi-processor PC, they couldn't perform any extended tests, so they never realized that their implementation had synchronization issues.

PS: For those who want to play at very high resolutions (e.g. 4k), the above won't be enough. The game will crash if the resolution is set too high. Luckily, you can get around that by using the software renderer. Simply add the following launch options:

-d:software -CPUPriority:high

"-CPUPriority:high" is needed because otherwise the game would be unplayable with software renderer. For some reason, the game renders at 0 FPS, and only gets to ~5 FPS if you focus on some other window. As soon as you try to interact with the game, the focus will return to it and it will render at 0 FPS again, so you have to constantly alt-tab whenever you click on something in the game.

By the way, a lot of people recommend using
-Cursors:fullcolor
as well, but I've yet to understand why it's needed and what it affects precisely.

For the record:
Each launch option starts with a dash (-) and is separated from the previous option with a whitespace ( ). You can add as many options as you want (as long as they're not contradictory, such as "-w" for windowed and "-f" for fullscreen mode), and their order usually doesn't matter.

If you wish to remove some launch options, remember to delete the "SimCity 4.cfg" file in your Documents folder (Documents\SimCity 4\SimCity 4.cfg). For instance, if you've used "-w" to run in windowed mode, you'll need to either replace it with "-f", or delete the .cfg file, otherwise you'll be stuck in windowed mode, even if you remove "-w".

Enjoy.