Yeah, emulators can enhance graphics pretty well, at the expense of CPU usage It's more noticably much nicer when emulating consoles that use 3D graphics though, since you can make the game render the 3D models at maybe 16x the detail so they look much better (when you compare dimensions of a monitor to TV).

I think the only game I've liked the Super Eagle engine for is Yoshi's Island though, with it's cartoony graphics, otherwise for most other games I prefer to have the video filters off and leave them pixelly. Plus it's actually better with them off for hi-res texture games like Tales of Phantasia, since you're not doing the artwork justice otherwise when you start to filter something already so detailed to the pixel level. I also believe the filters aren't good for games that use the special hi-res mode like Seiken Densetsu, and it can make the text rather unreadable, though I'll ahve to double check on that.