DominionPrime: Ah ha, changing the output to ddraw did the trick. Can stay in windowed mode and change the resolution that way. Thanks!
Now I wish I could pull the same trick with the '98 version. The lack of such options for it confuses me...
PatTheMav: Best solution for the 1998 version is to use the scaling available in nVidia/AMD control panels and selecting GPU scaling with keeping aspect ratio intact. Worked for me on my nVidia card, can't tell what exactly you need to configure for AMD GPUs.
For AMD in the catalyst control center the option for controlling aspect ratio is under:
My Digital Flat-Panels --->Properties --->Image Scaling Preferences
Unfortunately none of these options seem to do anything, supposedly if you set your desktop resolution to a non-native resolution and then scaling will work, it didn't for me, but it's worth try. Looking around it seems AMD regularly fixes then breaks these options in their various driver updates, but if you get it to work let us know, and tell us the driver version and OS you're using. I'm using driver version 14.7 on Vista64.