I use mostly linux ( i booted windows last time in november 2005 ).
Msx: openmsx imho is really good.
Pce: there is hugo and mednafen ( also emulates nes, lynx, gba and maybe something else ), the shareware emu for windows worked a pair of years ago with wine, iirc was called magic engine.
atari 2600: stella seems very good to me, there is also z26 but i have never tried it.
Spectrum: iirc fuse is quite good.
C64: vice, not that good in terms of interface.
If you want more info let me know.