I'm not sure exactly what you're trying to do, but you probably can sort of do it. You can use VNC to control another Mac. The other option is to use Synergy which is a mouse/keyboard sharing program. For example, I keep my PowerBook to the left of my iMac on my desk at home. I have Synergy set up so that my PowerBook seems like just another screen, and when I move the mouse off the left side of my iMac screen, it goes onto the PowerBook and the keyboard and mouse control the PowerBook. Move it back to the right and it switches back to the iMac.
Is that the kind of thing you're talking about? With VNC, you'd see the eMacs screen on your MBP in a window (or full screen if you want) and could control it remotely.
Of course, you can't run an application on your MBP then just drag the window accross to the eMac and have it start running on the eMac, or share the two processors or anything like that. But it is certainly possible to link the two so that using them at the same time is more comfortable.