E-UAE for MOS runs pretty well, there are two versions for MOS, a native compile with overlay support and a SDL compile. They both support joysticks.
The SDL version has fullscreen support but the native version is a bit faster but you can't go fullscreen and there's no Picasso support I believe. Most games/demos I tried in both versions work fullspeed and are very playable on my Pegasos II G4.
If you want to use Workbench with Picasso screenmodes the speed is about half of a real a4000, it feels a bit sluggish though. The most important thing missing is JIT, this would speed up things very much. There's also a gui but I didn't try it, I just edit the different uaerc config files I have and start E-UAE with the config file I need.
There's also a Linux live CD with E-UAE available for the Pegasos II, didn't try it so I cannot comment on that.
But, nothing beats a real Amiga to play games on, I only use E-UAE on MOS to play some demo's. I've got an a1200 setup with WHDLoad just for games

~tempest