perl -nle '/tilda/ && s/\[// && s/\]// && print qq{insert into mytable values(SEQ_MY_ID.nextval, "$_", "01",sysdate,"","")}' report.conf

That works as long as $_ doesn't contain double quotes, and your database engine has not problems with double quotes..

If you use double quotes on the outside, the shell tries to interpolate $_, so you have to escape it with a backslash: \$_

Quoting rules vary by shell, differing especially between Windows and Unix and Unix-like systems, e.g., Linux or cygwin. In *ixen, embedded single quotes can be escaped with a backslash. On *ixen, as in Perl, double-quoted strings will expand variables, which would include strings starting with dollar signs ($). This may not be what you want.

perl -nle '$q="\x27"; /tilda/ && s/\[// && s/\]// && print "insert int
+o mytable values(SEQ_MY_ID.nextval, $q$_$q, ${q}01$q,sysdate,$q$q,$q$
+q)"' report.conf
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The problem is more the spaces than the quotes. For example, in bash you sometimes see something like this:

if [[ x"$a" == x ]]; then
    # $a was empty, so do something
fi
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You can just put characters right beside the quotes like that. So focus more on the spaces than the quotes. The quotes you always see around a command are just there to protect the spaces! (plus single quotes obviously prevent variables from interpolating)

perl -le print\ \''hello world!\n'\'
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(That's like perl -le 'print 'hello world!\n'' except it works. :) The inner pair single-quotes are there just to keep the space and \n from being interpolated by the shell.)

try:

$_ =~ s|\"|\\"|g;
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