I want to modify the queries of a running application so that what's passed to the database includes a comment that tells where in the Perl code the request originated.

Well, there is such a thing as an SQL comment, and for at least some databases (e.g. MySQL), I believe the comments get logged along with the SQL. (There was one occasion where I solved a problem like this with screwed-up capitalization, e.g. changing "SELECT" to "SeLECT", "SElECT", "SELeCT"...).

Have you looked at the "TRACING" features listed in the DBI docs? That at least can be turned on dynamically, though if the docs are up-to-date, I infer that it doesn't have SQL logging yet:

       Curently the DBI only defines two trace flags:

         ALL - turn on all DBI and driver flags (not recommended)
         SQL - trace SQL statements executed (not yet implemented)
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Update: actually, I bet that turning on trace level 1 is pretty close to what you're asking for. It will echo your prepare statements (including the SQL), and label them with line number and file of your code:

  $dbh->trace(1, $trace_log_file);
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