That would be pretty trivial. If you had the Windows 3.0 source code, you could compile it, and the binaries you'd get would be the same as the shipped binaries. (Your version of the source code might not be exactly the same version as the shipped binaries, but even if not 100% identical, a binary diff or disassembly would should great similarity.) Even if someone has modified the code a bit, there would still be immense similarities there, which would be difficult to explain as anything other than copying.
Also, GeoWorks and Windows 3.0 have quite different APIs. If you find code exposing an API which is bug-for-bug-compatible with Windows 3.0, then it almost surely is a derivative of the real Windows 3.0 source code. It could be a derivative of some compatible implementation of the Windows API, such as Wine or Sun Wabi, but neither of those would be bug-for-bug compatible; and, as jerf pointed out, a defendant which claimed that they (or someone else other than Microsoft) wrote the code from scratch would have to provide some evidence that they (or someone else) actually carried out the Herculean task of creating a bug-for-bug compatible clean room clone of the Windows API. And not just the application-level API – Windows 3.x has heaps of internal APIs, which largely weren't used by applications and which newer Windows versions don't support (for example, the legacy Windows 3.x device driver models) – any modified copy of the Windows 3.x source is going to support all that, a clean room reimplementation is unlikely to do so. Courts decide civil cases on the basis of the balance of the probabilities, and such a claim must be viewed as improbable, unless some concrete positive evidence is put forward to demonstrate it is true.
(IANAL, but you don't need to be a lawyer to know that Microsoft would win this one.)