I cannot speak for everyone, nor can I speak in general, I can only relate as to my own personal experiences with SFC and Windows.
You asked about Windows ME or WinME. SFC has run fine on this OS for me. I have had no problems overall, I think I may have had a crash or two with SFC2 like a year or two ago. I have a slowdown bug with OP occasionally in the SP campaigns, that for some reason, never has gone away completely. I have had one crash some time ago (years again) when using a Mirak type against certain Klingon and Federation ships.
I have had far more problems with Windows XP Pro, and Home. These two systems, despite what others may tell me, have proven to be the worst OS for games I have encountered, and crash regularly in many of my games. It is no surprise then, that I have had problems with WinXP and the SFC series. In WinXP I have had the problem with SFC 2 where my buttons will not respond if started from the game from the shortcut. It had to be started from the exe or I have to do a switch to desktop and then reopen the game to get keyboard response. If I do that, I then got a big red square something instead of my mouse cursor. In SFC 3, I've encountered a crash bug where unless I save after every mission (and even then many times) in SP, the game will crash. This is really a pain for the Dynaverse (though I think it may be more of hardware related with the ATI cards, no offense intended to them, as the game as a whole is more stable even with XP with the Nvidia cards). There are multiple other bugs in SFC 3 with XP also pertaining to a never ending load time, a CTD, and more.
In addition, with XP, I've experienced with both SFC 3, and SFC 1, the point where it won't detect the CD. For SFC 3 this is due to XP's response to making you use the drive from which the game was installed.
As I stated these are personal experiences and probably do not reflect the general public as a whole as far as their thoughts and things that have happened with them and Various OS's.