I've only ever used WinUAE so can't be of much help I'm afraid, but apart from the aggravating and very poorly documented CD ROM issues I'm very satisfied with UAE's performance.
I can run all the legacy software I wish, simply by changing configuration to use different ROM files, hardware etc. Previosly I had four (A500 ks1.2, A500 ks1.3, A1200 ks3.0 and A1200, '040, 64Mb, Voodoo etc with ks3.1!) different Amigas which ran four different sets of software / demos. You can imagine the kerfuffle plugging in and swapping that lot was...
