I never saw in crashing of the Mac OS itself under FUSION, but there were plenty of apps that did not like superscaler and/or branch caches enabled. However, in all fairness these apps were written for the 020/030, so minimal cache flushing was required for self modifying code, which is quite common for decompression programs, encryption for copy protection, etc. Some of these issues could be due to buggy superscaler mode in early 060 revs. I went from the first rev available from Phase 5 to the PPC, so I never tested any newer revs.
I know that floating point math scores were often times faster with the 68040-33MHz X-Calibur board than the Cyberstorm 060-50MHz.
Sadly even a 75MHz 060 is really slow compared to modern Intel processors, so the idea of a dedicated Intel CPU adapter is probably the fastest and least expensive option.