I would like to keep the name "Nestopia" in the name, so it can identify back with the project...NestopiaX?
I don't know if NestoppiaX is easily confused with Bannister's port. People might see the X as a version indicator (i.e. OSX native / Cocoa) and not recognize it as a separate build.
From the earlier suggestions, I like OpenNestopia, for it best describes how the project differs from the other build - it's the open source variant. Also, having the name variation at the beginning instead of at the end will help establish the project as being separate. My opinion here - take it for what it's worth.