IBrowse, AmiNetRadio, MakeCD, AmiTradeCenter, AmTelnet, HBMonopoly, ReSource and bunch of old commandline tools. These are some of the m68k apps I still use. For some there are decent replacements already, but I still consider the actual Amiga apps better. For some there simply are no replacement.
Being forced to run those inside emulation would seriously suck (for me at least). Even with integration, how would the menus work? How about appwindows and appicons? How about accessing the filesystems (commandline tools)? How about MakeCD accessing the cd-rw drive for burning? How about inconsistent GUI look?