On balance I reckon an Amiga with an MMU works better with it, and with the patches it provides, than without, but if you have an obscure accelerator with special CPU libraries it's possible that Thor's mmu library might clash. However if you run emulators and/or use a Commodore CPU or a Phase 5 or Apollo 68K accelerator, it's probably going to make your system more stable and more capable.
My 2p - SimonG
http://www.amigacentre.co.uk/cgi-bin/wiki.pl/SimonGoodwinFor lots of excellent general advice on 68K Amiga stability, see:
http://simon.mooli.org.uk/AF/article/GOODWIN/GW02.HTML
