Okay, so I've been working all day on finding a solution to this problem I'm having. I used DeltaPatcher to patch Sonic 3D. Ver 0.1 worked since I downloaded it as a separate file since some kind-hearted soul managed to release a patched version of Sonic 3D with Ver0.1. However, when I tried patching (a clean rom of) Sonic 3D by myself, everything was working fine. The original file was patched and I was good to go. But then, Kega Fusion starts actin' up tellin' me I don't have the right file type (it's a .zip file, by the way). Anyways, Clearly, I'm not doing something right here and I've searched high and low for a solution. My best bet now is to hope that a gentile being will stumble upon my tragic story of the most depressing of plights.
TL;DR I tried patching Sonic 3D and Kega Fusion doesn't like it when I do that...I think...
Oh, yikes. One easy way to tell if you have a ROM file is to rename it to .bin and run it on Kega Fusion to see if it works. If you need a different file, someone could assist with a source, or you could purchase the game off of Steam.