Very true, I have edited the last post - not that it really makes a difference or anything. But I like those places and I'd hate to see them go away any time soon. I'm sure after a decade of being around, they are not going to go anywhere though. The only game I have noticed that is missing from some of the ROM sites is Sonic. And it's always the US version. For some reason the EU and JP versions are always present. So maybe SOA did contact some of those sites and just told them to take down the Sonic ROMS but not everything else cause they could care less about everything else.
Also, Sega really could only ask that THEIR roms be taken down. Everyone else like Konami and Capcom would probably have to do the same, specifically for their games. I am not sure if Sega has the rights to down a complete site, or just the files that belong to them.
In any case, I really think that we are over thinking this a bit. I really don't think it's an issue - at all.