I have it on my 98SE box, but I really only use it as a quick-and-easy fix for bypassing artificially-imposed incompatibilities... i.e., software that would otherwise run fine if it weren't for a version check in the installer or something.
With regards to running software that is actually incompatible with Win9x, I see it as more of a last resort, for cases where no Win9x-compatible programs exist with the functionality you need. And honestly, those cases are few and far between... generally, if there's something I need to do that no Win9x programs can do, it's something that wouldn't work too well on a Win98-era machine anyway. The trouble I've found is, while KernelEX will allow you to run programs that otherwise wouldn't run, more often than not the programs still won't work 100%, and it makes for some pretty frustrating glitches.