Version: (using KDE KDE 3.5.8) Installed from: SuSE RPMs ~ in URL is a valid character (and it is visible in Konqueror) yet KMail decides to convert it to %7E which is correct but a bit confusing (visually two different addresses in Konqueror and KMail).
I can't reproduce in kmail 1.9.10. Tried to paste url with ~ and also tried to send link from konqueror but link appears proper in both cases.