Unless it explicitly says otherwise C64 roms (and Amiga, Spectrum, CPC ... all the classic 'mostly' European home computer systems) are PAL and run at the correct speed and music pitch on an emulated PAL C64. The problem then becomes running a 50hz system against a fixed 60hz refresh rate LCD, causing jerky scrolling, which you solved by switching TV mode. 'Mostly' NTSC systems with NTSC romsets like SNES and Genesis need to run at 60hz though (otherwise it's jerky scrolling and wrong speed again, this time too slow), so there should be a way to dynamically switch refresh rate for each system. I'm working on it, but my bash scripting skills are low to non-existent :)
And yes, once you cross into 3D systems it's another ballgame completely.