I think what you're looking for is the /m modifier. This allows ^ and $ to match newlines in multiline data. Since it appears you need to worry about multiline queries (otherwise, why are you modifying the record separator in the first place), I changed your data to include one.
$/ = ";\n";
while (my $line = <DATA> ){
$line =~ s/^#[^\r\n]*//mg;
print "Query: $line\n";
}
__DATA__
# one comment
# two comment
# another comment
insert into table_name
values(1, 'testing 1 2 3');
# more comments
insert into table_name values (2, 'test •');
...gives...
Query:
insert into table_name
values(1, 'testing 1 2 3');
Query:
insert into table_name values (2, 'test •');
You could also add $line =~ s/^\s*$//mg; if you want to get rid of some of those blank lines.
-Bird
Update: I like
insensate's solution for removing the blank lines better. Use that one. :)