Well, I started this thread about it last month:
http://eab.abime.net/showthread.php?t=17480
But I have since found "Acvt" on Aminet which will convert atr to xfd quickly (without having to emulate DOS!). I use "acvt -classic -xfd -autorepair filename.atr".
So far, the only games I have been able to sucessfully run in ACE without major problems are:
Montezuma's Revenge (16K version)
Defender
Robotron
Qbert
Seafox
Zaxxon
Miner 2049er (but many enemies die when you kill one)
Boulderdash (scrolling is ugly)
Centipede 5200 (centipede sometimes leaves trails)