Same with me, I'll still instinctively go for ~. when a connection has hung / dropped (usually because of a NAT via a rebooted firewall), but never even considered how ~ doesn't normally cause an issue. Never knew it had to be immediately following a newline. Also never knew about the other options, ~^Z in particular looks useful.
I wonder if anyone still remembers the ctrl-[ sequence in telnet. I think I only ever used the quit command in that though.