Having heard quite a bit about what the OpenEmu team is doing and where the project's going, I think the name is a good one. But I'll admit that before I interviewed the team and tried the development builds I shared your concern.
I also remember when I first heard about Open Emulator—it must have been at least a year now—I got confused. I didn't know what it was, or how it differed from OpenEmu (to be brief, Open Emulator is a modularly-designed Apple-family emulator—currently focused on getting basic Apple I and Apple II emulation up to speed. It's very much for hackers and geeks, with huge potential for detailed customisation and extension. OpenEmu also has a modular, plugin-based design, but it's meant as an "everything" emulator with an emphasis on the user experience. It's the emulator we've all been waiting for, which finally cuts out the crap and makes playing old games simple.)
I understand the logic behind the Open Emulator name, but if anything is to be renamed I think that should be the one—even if it just gets the word "Apple" shoved in the middle. You'd never guess what it emulates from the name; you might have more luck guessing OpenEmu's scope.
It is pretty funny that they independently came up with what is effectively the same name, though.
