Though I've used both WinFellow and WinUAE, personally my own preference is WinUAE. Besides the fact that the emulation is more complete in a number of areas, I just like the way that it handles configurations better. Being the anal-retentive type, I prefer creating a separate configuration file that is optimized for each game, and then having a folder full of shortcuts to each config that will allow me to start each one by simply double clicking on the one I want. That's pretty simple to do with WinUAE, but I've never quite figured out how to do it using WinFellow.
Of course, being anal-retentive has a downside - namely that I find myself spending lots of time creating working configs for all those games, and having little time left to actually play them. But SOMEDAY, I'll be done with it, and can devote my time to trying to decide WHAT to play.
By the way, I currently have working configs for about 400 games, so if anybody is having trouble with finding a configuration that works for any specific title, I'd be more than happy to help out if it's one of the ones I've already gotten to work.