If a line terminator in $string is the source of your problems, your regex will not correct it. I believe you need to force the substitution to treat the string as a single line and then replace the characters that are potential problems. In some scenarios, it might be better to replace runs of line terminators with a space, though that will depend on context. Also, it would be better to assume that there may be more than one line terminator. Example:

#!/usr/bin/perl

$string = "foo
bar";

$string =~ s/\s+$//;
print $string, "\n\n";

$string =~ s/[\r\n]+/ /gs;
print $string, "\n\n";
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This produces:

foo
bar

foo bar
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NOTE: It is always dangerous to directly insert user input in a mail header; user input warrants careful scrutiny. The documentation on tainting in the perlsec reference is very helpful on this subject.