Amiga is not as good as on windows as WinUAE is just too damn fine.
It's true but E-UAE is trying to bring the benefits of WinUae to the Linux world. However there's still some stuff missing. Personally I find the missing vertical synchronisation the most annoying point, but that is of course mainly because I'm using it with an arcade monitor. Except of this you get a well running UAE with a similar GUI than WinUae. Give it a try, you can find it at http://rcdrummond.net/uae/
And finally the most important one - MAME. Linux has AdvanceMame and Xmame which are as good as their windows counterparts.